Increased seeds per POD in modified soybean

Abstract

The disclosure relates to novel soybean plants, plant parts, and nucleotide sequences in soybean plants comprising an amorphic or hypomorphic allele of a CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene, along with methods of using and making the same.

Description

TITLE: INCREASED SEEDS PER POD IN MODIFIED SOYBEANCROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims benefit under 35 U.S.C. § 119 to U.S. provisional patent application U.S. Serial No. 63 / 666,382, filed July 1, 2024; U.S. provisional patent application U.S. Serial No. 63 / 684,737, filed August 19, 2024; U.S. provisional patent application U.S. Serial No. 63 / 690,096, filed September 3, 2024; U.S. provisional patent application U.S. Serial No. 63 / 705,853, filed October 10, 2024; U.S. provisional patent application U.S. Serial No. 63 / 711,978, filed October 25, 2024; U.S. provisional patent application U.S. Serial No. 63 / 712,670, filed October 28, 2024; U.S. provisional patent application U.S. Serial No. 63 / 719,558, filed November 12, 2024; U.S. provisional patent application U.S. Serial No. 63 / 722,460, filed November 19, 2024; and U.S. provisional patent applications U.S. Serial Nos. 63 / 727,053 and 63 / 727,061, both filed December 2, 2024. Each of the aforementioned provisional patent applications are incorporated herein by reference in their entirety, including without limitation, the specification, claims, sequence listing, and abstract, as well as any figures, tables, appendices, or drawings thereof.SEQUENCE LISTING STATEMENT

[0002] instant application contains a sequence listing, which has been submitted in XML file format by electronic submission. The XML sequence listing file for this application was created on June 27, 2025, is named P14796WOOO.xml, is 352,582 bytes in size, and is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 684,737, which was created on July 30, 2024, is named P14880US00.xml, and is 22,627 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 666,382, which was created on June 10, 2024, is named P14796US00.xml, and is 13,974 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 727,061, which was created on November 21, 2024, is named P14861US00.xml, and is 18,575 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 719,558, which was created on November 4, 2024, is named P15019US00.xml, and is 27,508 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 705,853, which was created on October 7, 2024, named P14962US00.xml, and is 20,621 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 712,670, which was created on October25, 2024, named P14992US00.xml, and is 128,872 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 727,053, which was created on November 21, 2024, named P15001US00.xml, and is 24,495 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 722,460, which was created on November 16, 2024, named P15014US00.xml, and is 35,849 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 711,978, which was created on October 23, 2024, named P14990US00.xml, and is 38,183 bytes in size, is incorporated herein by reference in its entirety. The XML sequence listing file submitted in U.S. provisional application 63 / 690,096, which was created on August 20, 2024, named P14930US00.xml, and is 28,324 bytes in size, 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene along with methods of making the same (e.g., by growing a soybean plant or seed lot), and methods of using the same.BACKGROUND

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

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

[0006] Disclosed herein are soybean plant cells comprising an amorphic or hypomorphic allele of the endogenous: CRN gene comprising the DNA molecule of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene comprising the DNA molecule of SEQ ID NO: 11 or an allelicvariant thereof; A0C4 gene comprising the DNA molecule of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76 gene identified herein as the CYP76C-1 gene comprising the DNA molecule of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76 gene identified herein as the CYP76C-2 gene comprising the DNA molecule of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene comprising the DNA molecule of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene comprising the DNA molecule of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene comprising the DNA molecule of SEQ ID NO: 85, 91, or an allelic variant thereof; RPF1 gene comprising the DNA molecule of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or the endogenous soybean TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof. Soybean plant parts, including a stem, root, leaf, flower, pod, or seed, and soybean plants comprising the aforementioned soybean plant cells are also provided.

[0007] Also disclosed are plants or plant parts of elite soybean plants, cultivars, or varieties with increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield comprising: (i) an amorphic or hypomorphic allele of the: endogenous CRN gene comprising the DNA molecule of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene comprising the DNA molecule of SEQ ID NO: 11, or an allelic variant thereof; AOC4 gene comprising the DNA molecule of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene comprising the DNA molecule of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene comprising the DNA molecule of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene comprising the DNA molecule of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene comprising the DNA molecule of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene comprising the DNA molecule of SEQ ID NO: 85, 91, or an allelic variant thereof; RPF1 gene comprising the DNA molecule of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or the endogenous TCP5 gene comprising the DNA molecule of SEQ ID NO: 115, 121, or an allelic variant thereof; wherein the at least one amorphic or hypomorphic allele comprises at least one mutation in the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB- 1, KHZ1, PP2C, RPF1, and / or TCP5 gene; wherein the increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of the soybean plant or a soybean plant grown from the plant part is in comparison to a wild-type or control soybean plant lacking the amorphic or hypomorphic allele of (i) and optionally wherein the plants or plant parts of (i) further comprise (ii) a hypomorphic or amorphic allele of at least one of an AlPlOa, AlPlOb, BS1, BS2, FTla, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene.

[0008] Also disclosed are soybean plant cells, soybean plant parts, or soybean plants obtainable by the process comprising: (i) directing both: (a) a guide RNA (gRNA) molecule comprising aspacer RNA molecule which targets the: CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; A0C4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof; and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule to the genome of a target soybean plant cell; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at least one mutation in the CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; optionally wherein the gRNA targeting the genes comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 4, 5, 6, 14, 18, 19, 20, 28, 29, 30, 38, 39, 40, 48, 49, 50, 78, 79, 80, 88, 89, 90, 101, 102, 103, 118, 119, or 120.

[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) maturity, thereby producing the soybean seed lot, are provided.

[0010] Methods for generating the aforementioned soybean plant cells, soybean plant parts, or soybean plants comprising introducing at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof are provided.

[0011] Methods for increasing seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield in a soybean plant, comprising: introducing at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof are provided.

[0012] Methods for generating the aforementioned soybean plant cells, soybean plant parts, or soybean plants comprising: (i) screening a population of soybean plant cells, parts, or plants for the presence of the at least one mutation in the endogenous: CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 212, or an allelic variant thereof; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation in the CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof are provided.

[0013] 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.

[0014] Biological samples comprising one or more nucleic acids containing: (i) an amorphic or hypom orphic allele of the endogenous CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof; wherein the at least one amorphic or hypomorphic allele comprises at least one mutation in the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene; and optionally wherein the biological samples of (i) further comprise (ii) a hypomorphic or amorphic allele of at least one of an AlPlOa, AlPlOb, BS1, BS2, FTla, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene are also provided.

[0015] Gene editing systems comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that has 100% sequence identity to the endogenous soybean: CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof; HB- 1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof are provided. Also provided are expression cassettes comprising: a polynucleotide encoding CRISPR-Cas effector protein comprising a cleavage domain and the aforementioned guide RNA molecule. Use of the guide RNA molecule, the gene editing system, or the expression cassette to introduce at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof are also provided.

[0016] Methods for determining whether a soybean plant cell, plant part, or plant comprises at least one mutation of the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; or an allelic variant thereof; RPF1 gene of SEQ ID NO:98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof comprising: (i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 2, 7, 11, 12, 15, 16, 21, 25, 26, 31, 35, 36, 41, 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, 75, 76, 81, 85, 86, 91, 95, 98, 99, 104, 111, 115, 116, 121, or an allelic variant thereof; or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 2, 7, 11, 12, 15, 16, 21, 25, 26, 31, 35, 36, 41, 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, 75, 76, 81, 85, 86, 91, 98, 99, 104, 111, 115, 116, 121, or an allelic variant thereof; from the plant cell, plant part, or plant, wherein an insertion, deletion, and / or substitution of one or more nucleotides in the polynucleotide or RNA is indicative of the presence of the at least one mutation; and / or (ii) analyzing a polypeptide encoded by SEQ ID NO: 1, 2, 7, 11, 12, 15, 16, 21, 25, 26, 31, 35, 36, 41, 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, 75, 76, 81, 85, 86, 91, 98, 99, 104, 111, 115, 116, 121, a portion thereof, or an allelic variant thereof; wherein 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 are provided.

[0017] Methods for determining whether a soybean seed lot comprises soybean seed comprising at least one mutation of the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98,99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof comprising: (i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 2, 7, 9, 10, 11, 12, 15, 16, 21, 23, 24, 25, 26, 31, 33, 34, 35, 36, 41, 43, 44, 45, 46, 51, 55, 56, 58, 59, 60, 61, 63, 64, 65, 66, 68, 69, 70, 71, 73, 74, 75, 76, 81, 83, 84, 85, 86, 91, 93, 94, 95, 96, 97, 98, 99, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 121, 123, 124,125, or an allelic variant thereof; or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 2, 7, 9, 10, 11, 12, 15, 16, 21, 23, 24, 25, 26, 31, 33, 34, 35, 36, 41, 43, 44, 45, 46, 51, 55, 56, 58, 59, 60, 61, 63, 64, 65, 66, 68, 69, 70, 71, 73, 74, 75, 76, 81, 83, 84, 85, 86, 91, 93, 94, 95, 96, 97, 98, 99, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 121, 123, 124, 125, or an allelic variant thereof; from a sample of the soybean seed lot, wherein 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; and / or (ii) analyzing a polypeptide encoded by SEQ ID NO: 1, 2, 7, 11, 12, 15, 16, 21, 25, 26, 31, 35, 36, 41, 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, 75, 76, 81, 85, 86, 91, 95, 98, 99, 104, 111, 115, 116, and / or 121, or an allelic variant thereof; a polypeptide of SEQ ID NO: 3, 13, 17, 27, 37, 47, 57, 62, 67, 72, 77, 87, 100, and / or 117, a portion thereof, or an allelic variant thereof from a sample of the soybean seed lot, wherein 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 are provided.

[0018] Soybean genomes characterized by the fact that they comprise: (a) an amorphic or hypom orphic allele of the endogenous CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof; wherein the at least one amorphic or hypomorphic allele comprises at least one mutation in the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene; and optionally wherein the soybean genomes of (i) further comprise (ii) a hypomorphic or amorphic allele of at least one of an AlPlOa, AlPlOb, BS1, BS2, FTla, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene are provided.DESCRIPTION OF THE DRAWINGS

[0019] Figure 1 A-D shows the wild-type CRN gene of SEQ ID NO: 1 which encompasses the 5’ untranslated region (SEQ ID NO: 9), coding region (SEQ ID NO: 2), and 3’ untranslated regions (SEQ ID NO: 10). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 4, 5, and 6 are indicated.

[0020] Figure 2A-H shows the wild-type AML4 gene of SEQ ID NO: 11 and the encoded AML4 protein of SEQ ID NO: 13. The coding region (SEQ ID NO: 12), the 5’ and 3’ untranslated regions (UTRs), and a guide RNA target site (SEQ ID NO: 14) are indicated.

[0021] Figure 3 A, B, and C shows the wild-type AOC4 gene of SEQ ID NO: 15 which encompasses the 5’ untranslated region (SEQ ID NO: 23), coding region (SEQ ID NO: 16), and 3’ untranslated regions (SEQ ID NO: 24). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 18, 19, and 20 are indicated.

[0022] Figure 4A-C shows the wild-type CYP76C-1 gene of SEQ ID NO: 25 which encompasses the 5’ untranslated region (SEQ ID NO: 33), protein coding region (SEQ ID NO: 26), and 3’ untranslated regions (SEQ ID NO: 34). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 28-30 are indicated.

[0023] Figure 5A, B, and C shows the wild-type CYP76C-2 gene of SEQ ID NO: 35 which encompasses the 5’ untranslated region (SEQ ID NO: 43), protein coding region (SEQ ID NO: 36), and 3’ untranslated regions (SEQ ID NO: 44). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 38-40 are indicated.

[0024] Figure 6A-M shows the wild-type HB-1 gene of SEQ ID NO: 45 which encompasses the 5’ untranslated region (SEQ ID NO: 53), protein coding region (SEQ ID NO: 46), and 3’ untranslated regions (SEQ ID NO: 54). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 48-50 are indicated.

[0025] Figure 7A-F shows the wild-type KHZ1 gene of SEQ ID NO: 75 which encompasses the 5’ untranslated region (SEQ ID NO: 83), protein coding region (SEQ ID NO: 76), and 3’ untranslated regions (SEQ ID NO: 84). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 78-80 are indicated.

[0026] Figure 8A-G shows the wild-type PP2C gene of SEQ ID NO: 85 which encompasses the 5’ untranslated region (SEQ ID NO: 93), protein coding region (SEQ ID NO: 86), and 3’ untranslated regions (SEQ ID NO: 94). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 88-90 are indicated.

[0027] Figure 9A-E shows the wild-type RPF1 gene of SEQ ID NO: 98 which encompasses the 5’ untranslated region (SEQ ID NO: 106), protein coding region (SEQ ID NO: 99), and 3’ untranslated regions (SEQ ID NO: 107). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 101-103 are indicated.

[0028] Figure 10A-E shows the wild-type TCP5 gene of SEQ ID NO: 115 which encompasses the 5’ untranslated region (SEQ ID NO: 123 and 124), coding region (SEQ ID NO: 116), and 3’ untranslated region (SEQ ID NO: 125). The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 118-120 are indicated.DETAILED DESCRIPTION

[0029] 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.

[0030] 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.

[0031] 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).

[0032] 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).

[0033] 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).

[0034] As used herein, the terms “Cpfl” and “Casl2a” are used interchangeably to refer to the same RNA dependent DNA endonuclease (RdDe).

[0035] As used herein, a “cultivar” refers to a cultivated variety. A cultivar is generally developed using crossing, selfing, and / or selection and is maintained by any suitable method of propagation, through open pollination, selfing, or the like. Details of cultivar development can be found in “Principles of Cultivar Development” by Fehr, Macmillan Publishing Company (1993), which is incorporated herein by reference in its entirety.

[0036] 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.

[0037] 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.

[0038] 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.

[0039] As used herein, the term “fused” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For example, a crRNA (Direct repeat or “DR”) RNA is fused to a spacer RNA when the RNA comprising the crRNA and the spacer RNA can form a complex with a Cas nuclease and a DNA target (e.g., genomic DNA comprising a target gene) and promote cleavage of the DNA target.

[0040] 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.

[0041] 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.

[0042] As used herein, the term “isomorphic allele” refers to an allele of a gene having wildtype gene activity.

[0043] The term “isolated” as used herein means having been removed from its natural environment.

[0044] 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 nucleicacid 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).

[0045] As used herein, a “loss-of-function allele” can include an amorphic allele or a hypomorphic allele of a gene.

[0046] As used herein in the specification, the phrase “CRN gene”, “AML4 gene”, “AOC4 gene”, “CYP76C-1 gene”, “CYP76C-2 gene”, “HB-1 gene”, “KHZ1 gene”, “PP2C gene”, “RPF1 gene”, or “TCP5 gene” is understood to include: (i) a CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, or TCP5 gene alone or an amorphic allele thereof; or (ii) a CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, or TCP5 gene alone, an amorphic allele thereof, or a hypomorphic allele thereof, wherein the CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, or TCP5 genes, the amorphic allele, or the 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, AMIN, AOC4, BS1, BS2, CRN, CYP76C-1, CYP76C-2, FT la, HB-1, JAG1, JAG2, KHZ1, NF-YC4, PP2C, RIC1, RIC2, RPF1, TCP5, and / or TFLlb gene.

[0047] 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).

[0048] 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.

[0049] 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.

[0050] 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.

[0051] 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.

[0052] The present disclosure provides for soybean plant cells, plant parts including seed, plants, seed lots, and biological samples comprising an amorphic or hypomorphic allele of a CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene (z.e., comprising at least one loss-of-function mutation in the endogenous CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene). 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.

[0053] The target endogenous CRN gene comprises the genomic DNA of SEQ ID NO: 1 and allelic variants thereof located on soybean chromosome 8. 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). Allelic variants of an endogenous soybean CRN gene include variantswhich encode CRN 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: 3. Allelic variants of an endogenous soybean CRN 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 CRN gene are isomorphic alleles of the endogenous soybean CRN gene. The wild-type soybean CRN (also referred to as CORYNE and SOL2) gene encodes a CLAVATA3 / END0SPERM SURROUNDING REGION (CLE) heterodimer receptor complex. CRN is a member of the Leucine-rich repeat (LRR) receptor-like kinase (RLK)family which are the predominant players in CLE peptide recognition and involved in stem cell maintenance. Guo et al. Plant Biotechnology Journal (2015) 13, pp. 801-910).

[0054] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean CRN gene of SEQ ID NO: 1, 2, 7, 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 of the CRN gene of SEQ ID NO: 1, 2, 7, 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 CRN gene. The insertion, deletion, and / or substitution can be made anywhere in the CRN 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, or 3141 nucleotides) of the CRN gene of SEQ ID NO: 1, 7, 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 988-1901 and 2523-2835 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) of the CRN gene. In certain embodiments, the at least one mutation in the CRN 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 CRN gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of exon 1 (z.e., nucleotides 988-1901 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) or exon 2 (z.e., nucleotides 2523-2835 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 adeletion, 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, or 914 nucleotides) corresponding to nucleotides 988-1901 (z.e., within the first exon) of the CRN 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 1215, 1220, 1225, 1230, or 1235 to 1239, 1244, 1249, 1254, or 1259; (ii) nucleotides 1238, 1243, 1248, 1253, or 1258 to 1262, 1267, 1272, 1277, or 1282; or (iii) nucleotides 1801, 1806, 1811, 1816, or 1821 to 1825, 1830, 1835, 1840, or 1845 of the CRN 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 a deletion, an insertion, and / or substitution that results in a frameshift mutation and / or a nonsense mutation in the coding region of the CRN gene. In certain embodiments, mutations of the CRN gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the CRN gene. In certain embodiments, mutations of the CRN 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, 374, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580,581, 583, 584, 586, 587, 589, 590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608,610, 611, 613, 614, 616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637,638, 640, 641, 643, 644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665,667, 668, 670, 671, 673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703,704, 706, 707, 709, 710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731,733, 734, 736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760,761, 763, 764, 766, 767, 769, 770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788,790, 791, 793, 794, 796, 797, 799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817,818, 820, 821, 823, 824, 846, 847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, 845,847, 848, 850, 851, 853, 854, 856, 857, 859, 860, 862, 863, 865, 866, 868, 869, 871, 872, 874,875, 877, 878, 880, 881, 883, 884, 886, 887, 889, 890, 892, 893, 895, 896, 898, 899, 901, 902,904, 905, 907, 908, 910, 911, 913, 914 nucleotides of the endogenous soybean CRN gene of SEQ ID NO: 1 located at nucleotides 988-1901 (i.e., within the first exon) 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 1215, 1220, 1225, 1230, or 1235 to 1239, 1244, 1249, 1254, or 1259; (ii) nucleotides 1238, 1243, 1248, 1253, or 1258 to 1262, 1267, 1272, 1277, or 1282; or (iii) nucleotides 1801, 1806, 1811, 1816, or 1821 to 1825, 1830, 1835, 1840, or 1845 of the CRN gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1.

[0056] 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 CRN protein while removing at least one, two, three codons, thus resulting in a mutant CRN protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the CRN gene can comprise a deletion of any number of nucleotides that are divisible by 3 in an exon of the CRN gene. In certain embodiments, the at least one mutation of the CRN 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, 555, 558, 561, 564, 567, 570,573, 576, 579, 582, 585, 588, 591, 594, 597, 600, 603, 606, 609, 612, 615, 618, 621, 624, 627,630, 633, 636, 639, 642, 645, 648, 651, 654, 657, 660, 663, 666, 669, 672, 675, 678, 681, 684,687, 690, 693, 696, 699, 702, 705, 708, 711, 714, 717, 720, 723, 726, 729, 732, 735, 738, 741,744, 747, 750, 753, 756, 759, 762, 765, 768, 771, 774, 777, 780, 783, 786, 789, 792, 795, 798,801, 804, 807, 810, 813, 816, 819, 822, 825, 828, 831, 834, 837, 840, 843, 846, 849, 852, 855,858, 861, 864, 867, 870, 873, 876, 879, 882, 885, 888, 891, 894, 897, 900, 903, 906, 909, or 912 nucleotides of the endogenous soybean CRN gene of SEQ ID NO: 1 located at nucleotides 988- 1901 (z.e., within the first 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 mutation comprises an internal deletion of at least 3 nucleotides corresponding to nucleotides 1215, 1220, 1225, 1230, or 1235 to 1239, 1244, 1249, 1254, or 1259 or nucleotides 1238, 1243, 1248, 1253, or 1258 to 1262, 1267, 1272, 1277, or 1282, or nucleotides 1801, 1806, 1811, 1816, or 1821 to 1825, 1830, 1835, 1840, or 1845 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 77, 78, 79, 80, 81, 82, or 83 to 84, 85, 86, 87, 88, 89, or 90, or amino acids 85, 86, 87, 88, 89, 90, or 91 to 92, 93, 94, 95, 96, 97, or 98, or amino acids 272, 273, 274, 275, 276, 277, or 278 to 280, 281, 282, 283, 284, 285, or 286 of SEQ ID NO: 3 or an allelic variant thereof which preserves the reading frame.

[0057] The target endogenous AML4 gene comprises the genomic DNA of SEQ ID NO: 11 and allelic variants thereof located on soybean chromosome 8. The endogenous soybean AML4 gene is 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). Allelic variants of an endogenous soybean AML4 gene include variants which encode AML4 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: 13. Allelic variants of an endogenous soybean AML4 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: 11. In certain embodiments, allelic variants of the endogenous soybean AML4 gene are isomorphic alleles of the endogenous soybean AML4 gene. The wild-type soybean AML4 (also referred to as MEI2-Like 4) gene encodes a mei2-like protein. Members of the mei2-like gene family encode RNA binding proteins with the characteristic presence of a highlyconserved RNA binding motif first described in the mei2 gene of the fission yeast Schizosaccharomyces pombe (Watanabe et al. EMBO J (1988) 7:761-7; Kaur et al. Plant Cell (2006) 18:545-59).

[0058] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean AML4 gene of SEQ ID NO: 11, 12, 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 of the AML4 gene of SEQ ID NO: 11, 12, 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 AML4 gene. The insertion, deletion, and / or substitution can be made anywhere in the AML4 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, 6000, 6500, or 6959 nucleotides) of the AML4 gene of SEQ ID NO: 11, 12, or an 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 (i.e., nucleotides 1071-1148, 1281-1326, 2158-2298, 2458- 2928, 3008-3406, 3596-4187, 5146-5230, 5634-5702, 5829-6008, and 6168-6323 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11 or 12) of the AML4 gene. In certain embodiments, the at least one mutation in the AML4 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 AML4 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of exon 1 (z.e., nucleotides 1 to 399 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 2 (z.e., nucleotides 1009 to 1148 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 3 (z.e., nucleotides 1281 to 1326 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 4 (z.e., nucleotides 2158 to 2298 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 5 (z.e., nucleotides 2458 to 2928 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 6 (z.e., nucleotides 3008 to 3406 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 7 (z.e., nucleotides 3596 to 4187 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 8 (z.e., nucleotides 5146 to 5230 of SEQ ID NO: 11 orin an equivalent position of an allelic variant of SEQ ID NO: 11), exon 9 (z.e., nucleotides 5634 to 5702 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), exon 10 (z.e., nucleotides 5829 to 6008 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11), or exon 11 (z.e., nucleotides 6168 to 6959 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11). 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, or 471 nucleotides) corresponding to nucleotides 2458 to 2925 (z.e., within the fifth exon) of the AML4 gene of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11). 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, or 25 nucleotides) corresponding to nucleotides 2604, 2609, 2614, 2619, or 2624 to 2628, 2633, 2638, 2643, or 2648 of the AML4 gene of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11 or 12.

[0059] 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 AML4 gene. In certain embodiments, mutations of the AML4 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the AML4 gene. In certain embodiments, mutations of the AML4 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, 374, 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, or 470 nucleotides of the endogenous soybean AML4 gene of SEQ ID NO: 11 located at nucleotides 2458 to 2928 (z.e., within the fifth exon) of SEQ ID NO: 11 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 nucleotides 2604, 2609, 2614, 2619, or 2624 to 2628, 2633, 2638, 2643, or 2648 of the AML4 gene of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11 or 12.

[0060] 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 AML4 protein while removing at least one, two, three codons, thus resulting in a mutant AML4 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the AML4 gene can comprise a deletion of any number of nucleotides that are divisible by 3 in an exon of the AML4 gene. In certain embodiments, the at least one mutation of the AML4 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, or 471 nucleotides of the endogenous soybean AML4 gene of SEQ ID NO: 11 located at nucleotides 2458 to 2928 (z.e., within the fifth exon) of SEQ ID NO: 11 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3 nucleotides corresponding to nucleotides 2604, 2609, 2614, 2619, or 2624 to 2628, 2633, 2638, 2643, or 2648 of SEQ ID NO: 11 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 138, 139, 140, 141, 142, 143, or 144 to 146, 147, 148, 149, 150, 151, or 152 of SEQ ID NO: 13 or an allelic variant thereof which preserves the reading frame.

[0061] The target endogenous soybean allene oxide cyclase 4 (AOC4) gene comprises the genomic DNA of SEQ ID NO: 15 (depicted in Figure 3A-C) and allelic variants thereof located on soybean chromosome 8. The endogenous soybean AOC4 gene is located at nucleotides 23,144,163-23,146,035 on the positive strand of chromosome 8 of the Glycine max Williams 82genome assembly version 4 (Wm82.a4.vl; Glyma.08G256600 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). Allelic variants of an endogenous soybean AOC4 gene include variants which encode AOC4 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: 13. Allelic variants of an endogenous soybean AOC4 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: 15, 16, or 21. In certain embodiments, allelic variants of the endogenous soybean AOC4 gene are isomorphic alleles of the endogenous soybean AOC4 gene. In certain embodiments, guide RNAs comprising the spacers encoded by SEQ ID NO: 18, 19, and 20 are used in conjunction with suitable Cas nucleases (e.g., a Type V Cas nuclease) to introduce amorphic or hypomorphic mutations in an exon which contains an open reading frame (ORF) encoding a portion of the AOC4 protein. In other embodiments, distinct gRNAs can be used to introduce amorphic or hypomorphic mutations in the AOC4 gene or allelic variants thereof.

[0062] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean AOC4 gene of SEQ ID NO: 15, 16, 21, 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 of the AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous AOC4 gene. The insertion, deletion, and / or substitution can be made anywhere in the AOC4 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, or 1873 nucleotides) of the AOC4 gene of SEQ ID NO: 15, 21, or an 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 342-591, 695-816, and 1254-1655 of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15) of the AOC4 gene. In certain embodiments, the at least one mutation in the AOC4 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 AOC4 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of anA0C4 protein coding region (e.g., nucleotides 342-591, 695-816, and 1254-1655 of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15). In certain embodiments, the at least one mutation in the A0C4 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of an A0C4 N- terminal protein coding region (e.g., nucleotides 342-591 of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15). 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, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, or 402 nucleotides) corresponding to nucleotides 342-591, 695-816, and 1254-1655 within the protein coding region of the AOC4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15. 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 337-361; (ii) nucleotides 382-406; or (iii) nucleotides 418-442; all of the AOC4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15.

[0063] 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 AOC4 gene. In certain embodiments, mutations of the AOC4 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the AOC4 gene (e.g., an exon located between nucleotides 342-591, 695-816, and 1254-1655 of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15). In certain embodiments, mutations of the AOC4 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, 374, 376, 377, 379, 380, 382, 383, 385, 386,388, 389, 391, 392, 394, 395, 397, 398, 400, or 401 nucleotides of an exon located in the endogenous soybean AOC4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15 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 337-361; (ii) nucleotides 382-406; or (iii) nucleotides 418-442; all of the AOC4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15.

[0064] 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 AOC4 protein while removing at least one, two, three codons, thus resulting in a mutant AOC4 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the AOC4 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 AOC4 gene. In certain embodiments, the at least one mutation of the AOC4 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, or 402 nucleotides in a protein coding region of an exon of SEQ ID NO: 15 or at an equivalent position in an allelic variant of SEQ ID NO: 15 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 337-361, 382-406, or 418-442 of SEQ ID NO: 15 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: (i) amino acids 1, 2, 3, 4, 5, 6, 7, 8, 9, and / or 10; (ii) amino acids 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, and / or 25; and / or (iii) amino acids 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, and / or 37; all of SEQ ID NO: 17 or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0065] The target endogenous soybean Cytochrome P450 superfamily protein (CYP76C-1) gene comprises the genomic DNA of SEQ ID NO: 25 (depicted in Figure 4A-D) and allelic variants thereof located on soybean chromosome 10. The endogenous soybean CYP76C-1 gene islocated at nucleotides 51,395,301-51,397,516 on the positive strand of chromosome 10 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.l0G296400 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). Allelic variants of an endogenous soybean CYP76C-1 gene include variants which encode CYP76C-1 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: 27. Allelic variants of an endogenous soybean CYP76C-1 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: 25 or 31. In certain embodiments, allelic variants of the endogenous soybean CYP76C-1 gene are isomorphic alleles of the endogenous soybean CYP76C-1 gene. In certain embodiments, guide RNAs comprising the spacers encoded by SEQ ID NO: 28, 29, and 30 are used in conjunction with suitable Cas nucleases to introduce amorphic or hypomorphic mutations in an exon which contains an open reading frame (ORF) encoding a portion of the CYP76C-1 protein. In other embodiments, distinct gRNAs can be used to introduce amorphic or hypomorphic mutations in the CYP76C-1 gene or allelic variants thereof.

[0066] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean CYP76C-1 gene of SEQ ID NO: 25, 26, 31, 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 of the CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous CYP76C-1 gene. The insertion, deletion, and / or substitution can be made anywhere in the CYP76C-1 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2216 nucleotides) of the CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an 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 142-1044 and 1199- 1828 of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25) of the CYP76C-1 gene. In certain embodiments, the at least one mutation in the CYP76C-1 gene can comprise a deletion of the entire coding region or any portion of the coding region requiredfor biological activity. In certain embodiments, the at least one mutation in the CYP76C-1 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) an N-terminal CYP76C-1 protein coding region (e g., nucleotides 142-1044 of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25). 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, 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, or 903 nucleotides) corresponding to nucleotides 142-1044 and 1199-1828 within the protein coding region of the CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25. 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 294-318; (ii) nucleotides 453- 477; or (iii) nucleotides 557-581; all of the CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25.

[0067] 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 CYP76C-1 gene. In certain embodiments, mutations of the CYP76C-1 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the CYP76C-1 gene (e.g, an exon located between nucleotides 142-1044 and 1199-1828 of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25). In certain embodiments, mutations of the CYP76C-1 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, 374, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580,581, 583, 584, 586, 587, 589, 590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608,610, 611, 613, 614, 616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637,638, 640, 641, 643, 644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665,667, 668, 670, 671, 673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703,704, 706, 707, 709, 710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731,733, 734, 736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760,761, 763, 764, 766, 767, 769, 770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788,790, 791, 793, 794, 796, 797, 799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817,818, 820, 821, 823, 824, 846, 847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, 845,847, 848, 850, 851, 853, 854, 856, 857, 859, 860, 862, 863, 865, 866, 868, 869, 871, 872, 874,875, 877, 878, 880, 881, 883, 884, 886, 887, 889, 890, 892, 893, 895, 896, 898, 899, 901, or 902 nucleotides of an exon located in the endogenous soybean CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25 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 294-318; (ii) nucleotides 453-477; or (iii) nucleotides 557-581; all of the CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25.

[0068] 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 CYP76C-1 protein while removing at least one, two, three codons, thus resulting in a mutant CYP76C-1 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the CYP76C-1 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 CYP76C-1 gene. In certain embodiments, the at least one mutation of the CYP76C-1 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, 555, 558, 561, 564, 567, 570, 573, 576, 579, 582,585, 588, 591, 594, 597, 600, 603, 606, 609, 612, 615, 618, 621, 624, 627, 630, 633, 636, 639,642, 645, 648, 651, 654, 657, 660, 663, 666, 669, 672, 675, 678, 681, 684, 687, 690, 693, 696,699, 702, 705, 708, 711, 714, 717, 720, 723, 726, 729, 732, 735, 738, 741, 744, 747, 750, 753,756, 759, 762, 765, 768, 771, 774, 777, 780, 783, 786, 789, 792, 795, 798, 801, 804, 807, 810,813, 816, 819, 822, 825, 828, 831, 834, 837, 840, 843, 846, 849, 852, 855, 858, 861, 864, 867,870, 873, 876, 879, 882, 885, 888, 891, 894, 897, 900, or 903 nucleotides in a protein coding region of an exon of SEQ ID NO: 25 or at an equivalent position in an allelic variant of SEQ ID NO: 25 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 294- 318, 453-477, or 557-581 of SEQ ID NO: 25 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: (i) amino acids 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, and / or 63; (ii) amino acids 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, and / or 116; and / or (iii) amino acids 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, and / or 150; all of SEQ ID NO: 27 or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0069] The target endogenous soybean transcription factor CYP76C-2 gene comprises the genomic DNA of SEQ ID NO: 35 and allelic variants thereof located on soybean chromosome 10 and depicted in Figure 5A-C. The endogenous soybean CYP76C-2 gene is located at nucleotides 51,262,793 to 51,265,190 of chromosome 18 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.l8G222900 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). Allelic variants of an endogenous soybean CYP76C-2 gene include variants which encode CYP76C-2 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: 37. Allelic variants of an endogenous soybean CYP76PC-2 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% sequenceidentity to SEQ ID NO: 35. In certain embodiments, allelic variants of the endogenous soybean CYP76C-2 gene are isomorphic alleles of the endogenous soybean CYP76C-2 gene.

[0070] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean CYP76C-2 gene of SEQ ID NO: 35, 36, 41, 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 of the CYP76C-2 gene of SEQ ID NO: 35, 36, 41, 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 CYP76C-2 gene. The insertion, deletion, and / or substitution can be made anywhere in the CYP76C-2 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, 2398 nucleotides) of the CYP76C-2 gene of SEQ ID NO: 35, 41, 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 (i.e., nucleotides 60-971 of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35) of the CYP76C-2 gene. In certain embodiments, the at least one mutation in the CYP76C-2 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 CYP76C-2 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) an N- terminal CYP76C-2 protein coding region (e g., nucleotides 60-971 or 1471-2082 of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35) or in an equivalent position of an allelic variant of SEQ ID NO: 35). 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, 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, or 971 nucleotides) corresponding to nucleotides 60-2082 (i.e., within the protein and intron coding region) of the CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35. 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 149-173; (n) nucleotides 239-263; or (in) nucleotides 292-316; all of the CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35.

[0071] 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 CYP76C-2 gene. In certain embodiments, mutations of the CYP76C-2 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the CYP76C-2 gene (e.g., the exons located between nucleotides 60-2082 of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35). In certain embodiments, mutations of the CYP76C-2 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, 374, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580, 581, 583, 584, 586, 587, 589, 590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608, 610, 611, 613, 614, 616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637, 638, 640, 641, 643, 644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665, 667, 668, 670, 671, 673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703, 704, 706, 707, 709, 710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731, 733, 734,736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760, 761, 763,764, 766, 767, 769, 770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788, 790, 791,793, 794, 796, 797, 799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817, 818, 820,821, 823, 824, 846, 847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, 845, 847, 848,850, 851, 853, 854, 856, 857, 859, 860, 862, 863, 865, 866, 868, 869, 871, 872, 874, 875, 877,878, 880, 881, 883, 884, 886, 887, 889, 890, 892, 893, 895, 896, 898, 899, 901, 902, 904, 905,907, 908, 910, and 911 nucleotides of an exon located in the endogenous soybean CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35 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 149-173; (ii) nucleotides 239-263; or (iii) nucleotides 292-316; all of the CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35.

[0072] 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 CYP76C-2 protein while removing at least one, two, three codons, thus resulting in a mutant CYP76C-2 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the CYP76C-2 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 CYP76C-2 gene. In certain embodiments, the at least one mutation of the CYP76C-2 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, 555, 558, 561, 564, 567, 570, 573, 576, 579, 582,585, 588, 591, 594, 597, 600, 603, 606, 609, 612, 615, 618, 621, 624, 627, 630, 633, 636, 639,642, 645, 648, 651, 654, 657, 660, 663, 666, 669, 672, 675, 678, 681, 684, 687, 690, 693, 696,699, 702, 705, 708, 711, 714, 717, 720, 723, 726, 729, 732, 735, 738, 741, 744, 747, 750, 753,756, 759, 762, 765, 768, 771, 774, 777, 780, 783, 786, 789, 792, 795, 798, 801, 804, 807, 810,813, 816, 819, 822, 825, 828, 831, 834, 837, 840, 843, 846, 849, 852, 855, 858, 861, 864, 867,870, 873, 876, 879, 882, 885, 888, 891, 894, 897, 900, 903, 906, 909, and 912 in a proteincoding region of an exon of SEQ ID NO: 35 or at an equivalent position in an allelic variant of SEQ ID NO: 35 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of SEQ ID NO: 35 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 28, 30, 32, or 34 to 35, 37, 39 or 41 , or amino acids 58, 60, 62, or 64 to 66, 68, 69, or 71, or amino acids 75, 77, 80, or 82 to 84, 86, 88, or 89 of SEQ ID NO: 37 or an allelic variant thereof which preserves the reading frame.

[0073] The target endogenous soybean sequence-specific DNA binding transcription factor Homeobox-1 (HB-1) gene comprises the genomic DNA of SEQ ID NO: 45 (depicted in Figure 6A-O), SEQ ID NO: 55 (an allelic variant of SEQ ID NO: 45), SEQ ID NO: 60, SEQ ID NO: 65, SEQ ID NO: 70 (shorter versions of SEQ ID NO: 55), and allelic variants thereof located on soybean chromosome 8. The endogenous soybean HB-1 gene is located at nucleotides 37,301,325- 37,311,393 on the negative strand of chromosome 7 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.07G201200 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). Allelic variants of an endogenous soybean HB-1 gene include variants which encode HB-1 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: 47, 57, 62, 65, and 72. Allelic variants of an endogenous soybean HB-1 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: 45, 51, 55, 60, 65, or 70. HB-1 gene transcripts comprising distinct genomic, coding, polypeptide 5’ UTR, and 3’UTR sequences, are disclosed herein (SEQ ID NO: 45, 46, 47, 53, and 54) and in sequence databases (Glyma.07G201200.1 (SEQ ID NO: 55, 56, 57, 58, and 59), Glyma.07G201200.2 (SEQ ID NO: 60, 61, 62, 63, and 64), Glyma.07G201200.3 (SEQ ID NO: 65, 66, 67, 68, and 69), Glyma.07G201200.4 (SEQ ID NO: 70, 71, 72, 73, and 74). In certain embodiments, allelic variants of the endogenous soybean HB- 1 gene are isomorphic alleles of the endogenous soybean HB-1 gene. In certain embodiments, guide RNAs comprising the spacers encoded by SEQ ID NO: 48, 49, and 50 are used in conjunction with suitable Cas nucleases to introduce amorphic or hypomorphic mutations in an exon which contains an open reading frame (ORF) encoding a portion of the HB-1 protein. In other embodiments, distinct gRNAs can be used to introduce amorphic or hypomorphic mutations in the HB-1 gene or allelic variants thereof.

[0074] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, 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 of the HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous HB-1 gene. The insertion, deletion, and / or substitution can be made anywhere in the HB-1 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10010 nucleotides) of the HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an 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 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45) of the HB-1 gene. In certain embodiments, the at least one mutation in the HB-1 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 HB-1 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) an N-terminal HB-1 protein coding region (e , nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, and 3228-3308 of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45). 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, 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, or 846 nucleotides) corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414- 3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631- 7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 nucleotides) within the protein coding region of the HB-1 gene of SEQ ID NO: 45 or in an equivalent position of an allelic variant ofSEQ ID NO: 45. 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 2720-2744; (ii) nucleotides 2809-2833; or (iii) nucleotides 2955-2979; all of the HB-1 gene of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45.

[0075] 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 HB-1 gene. In certain embodiments, mutations of the HB-1 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the HB-1 gene (e.g., an exon located between nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45). In certain embodiments, mutations of the HB-1 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, 374, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580, 581, 583, 584, 586, 587, 589,590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608, 610, 611, 613, 614, 616, 617,619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637, 638, 640, 641, 643, 644, 646,647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665, 667, 668, 670, 671, 673, 674,676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703, 704, 706, 707, 709, 710, 712,713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731, 733, 734, 736, 737, 739, 740,742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760, 761, 763, 764, 766, 767, 769,770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788, 790, 791, 793, 794, 796, 797,799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817, 818, 820, 821, 823, 824, 846,847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, or 845 nucleotides of an exon located in the endogenous soybean HB-1 gene of SEQ ID NO: 45, 55, 60, 65, or 70, or in an equivalent position of an allelic variant of SEQ ID NO: 45, 55, 60, 65, or 70, 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 2720-2744; (ii) nucleotides 2809-2833; or (iii) nucleotides 2955-2979; all of the HB-1 gene of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45.

[0076] 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 HB-1 protein while removing at least one, two, three codons, thus resulting in a mutant HB-1 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the HB-1 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 HB-1 gene. In certain embodiments, the at least one mutation of the HB-1 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, 552,555, 558, 561, 564, 567, 570, 573, 576, 579, 582, 585, 588, 591, 594, 597, 600, 603, 606, 609,612, 615, 618, 621, 624, 627, 630, 633, 636, 639, 642, 645, 648, 651, 654, 657, 660, 663, 666,669, 672, 675, 678, 681, 684, 687, 690, 693, 696, 699, 702, 705, 708, 711, 714, 717, 720, 723,726, 729, 732, 735, 738, 741, 744, 747, 750, 753, 756, 759, 762, 765, 768, 771, 774, 777, 780,783, 786, 789, 792, 795, 798, 801, 804, 807, 810, 813, 816, 819, 822, 825, 828, 831, 834, 837, 840, 843, or 846 nucleotides in a protein coding region of an exon of SEQ ID NO: 45, 55, 60, 65, or 70, or at an equivalent position in an allelic variant of SEQ ID NO: 45, 55, 60, 65, or 70, and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 2720-2744, 2809- 2833, or 2955-2979 of SEQ ID NO: 45 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: (i) amino acids 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, and / or 254; (ii) amino acids 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, and / or 284; and / or (iii) amino acids 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, and / or 332; all of SEQ ID NO: 47, 57, 62, 67, 72, or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0077] The target endogenous soybean zinc finger CCCH domain-containing protein 14 (KHZ1) gene comprises the genomic DNA of SEQ ID NO: 75 (depicted in Figure 7A-F) and allelic variants thereof located on soybean chromosome 10. The endogenous soybean KHZ1 gene is located at nucleotides 51,415,144-51,419,912 on the negative strand of chromosome 10 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.10G296700 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). Allelic variants of an endogenous soybean KHZ1 gene include variants which encode KHZ1 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: 77. Allelic variants of an endogenous soybean KHZ1 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: 75 or 81. In certain embodiments, allelic variants of the endogenous soybean KHZ1 gene are isomorphic alleles of the endogenous soybean KHZ1 gene. In certain embodiments, guide RNAs comprising the spacers encoded by SEQ ID NO: 78, 79, and 80 are used in conjunction with suitable Cas nucleases to introduce amorphic or hypomorphic mutations in an exon which contains an open reading frame (ORF) encoding a portion of the KHZ1 protein. In other embodiments, distinct gRNAs can be used to introduce amorphic or hypomorphic mutations in the KHZ1 gene or allelic variants thereof.

[0078] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean KHZ1 gene of SEQ ID NO: 75, 81, 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 of the KHZ1 gene of SEQ ID NO: 75, 76,81, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous KHZ1 gene. The insertion, deletion, and / or substitution can be made anywhere in the KHZ1 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, or 4769 nucleotides) of the KHZ1 gene of SEQ ID NO: 75, 76, 81, or an 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 205-274, 684-744, and 3855-4617 of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75) of the KHZ1 gene. In certain embodiments, the at least one mutation in the KHZ1 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 KHZ1 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) a KHZ1 protein coding region (e.g., nucleotides 205-274, 684-744, and 3855-4617 of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75). 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, 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, or 763 nucleotides) corresponding to nucleotides 205-274, 684-744, and 3855-4617 within the protein coding region of the KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75. 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 230-254; (ii) nucleotides 715-739; or (iii) nucleotides 3943-3967; all of the KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75.

[0079] 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 KHZ1 gene. In certain embodiments, mutations of the KHZ1 gene can comprise a deletion of any number of nucleotides that are notdivisible by 3 in an exon of the KHZ1 gene (e.g., an exon located between nucleotides 205-274, 684-744, and 3855-4617 of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75). In certain embodiments, mutations of the KHZ1 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, 374, 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, 554, 556, 557,559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580, 581, 583, 584, 586,587, 589, 590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608, 610, 611, 613, 614,616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637, 638, 640, 641, 643,644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665, 667, 668, 670, 671,673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703, 704, 706, 707, 709,710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731, 733, 734, 736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760, 761, 763 nucleotides of an exon located in the endogenous soybean KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75 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 230-254; (ii) nucleotides 715- 739; or (iii) nucleotides 3943-3967; all of the KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75.

[0080] 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 KHZ1 protein while removing at least one, two, three codons, thus resulting in a mutant KHZ1 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the KHZ1 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 KHZ1 gene. In certain embodiments, the at least one mutation of the KHZ1 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, 552,555, 558, 561, 564, 567, 570, 573, 576, 579, 582, 585, 588, 591, 594, 597, 600, 603, 606, 609,612, 615, 618, 621, 624, 627, 630, 633, 636, 639, 642, 645, 648, 651, 654, 657, 660, 663, 666,669, 672, 675, 678, 681, 684, 687, 690, 693, 696, 699, 702, 705, 708, 711, 714, 717, 720, 723,726, 729, 732, 735, 738, 741, 744, 747, 750, 753, 756, 759, 762 nucleotides in a protein coding region of an exon of SEQ ID NO: 75 or at an equivalent position in an allelic variant of SEQ ID NO: 75 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of SEQ ID NO: 75 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: (i) amino acids 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and / or 20; (ii) amino acids 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, and / or 44; and / or (iii) amino acids 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, and / or 85; all of SEQ ID NO: 77 or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0081] The target endogenous soybean protein phosphatase type 2C (PP2C) gene comprises the genomic DNA of SEQ ID NO: 85 (depicted in Figure 8A-J) and allelic variants thereof located on soybean chromosome 10. Allelic variants of SEQ ID NO: 85 include SEQ ID NO: 95, an allelic variant of SEQ ID NO: 85 comprising distinct 5’ UTR and 3’ UTR sequences. The endogenous soybean PP2C gene is located at nucleotides 51,042,872-51,048,930 on the positivestrand of chromosome 10 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.l0G291800 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). Allelic variants of an endogenous soybean PP2C gene include variants which encode PP2C 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: 87. Allelic variants of an endogenous soybean PP2C 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: 85 or 91. In certain embodiments, allelic variants of the endogenous soybean PP2C gene are isomorphic alleles of the endogenous soybean PP2C gene. In certain embodiments, guide RNAs comprising the spacers encoded by SEQ ID NO: 88, 89, and 90 are used in conjunction with suitable Cas nucleases to introduce amorphic or hypomorphic mutations in an exon which contains an open reading frame (ORF) encoding a portion of the PP2C protein. In other embodiments, distinct gRNAs can be used to introduce amorphic or hypomorphic mutations in the PP2C gene or allelic variants thereof.

[0082] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean PP2C gene of SEQ ID NO: 85, 91, 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 of the PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous PP2C gene. The insertion, deletion, and / or substitution can be made anywhere in the PP2C 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000, 5250, 5500, 5750, or 6059 nucleotides) of the PP2C gene of SEQ ID NO: 85, 86, 91, or an 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 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85) of the PP2C gene. In certain embodiments, the at least one mutation in the PP2C 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 PP2C gene comprises, consistsessentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of a PP2C protein coding region (e.g., nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, and 3717-3803 of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85). 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, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, or 182 nucleotides) corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, and 3717-3803 within the protein coding region of the PP2C gene of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85. 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 3097-3121; (ii) nucleotides 3296-3320; or (iii) nucleotides 3734-3758; all of the PP2C gene of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85.

[0083] 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 PP2C gene. In certain embodiments, mutations of the PP2C gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the PP2C gene (e.g., an exon located between nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85). In certain embodiments, mutations of the PP2C 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, or 182 nucleotides of an exon located in the endogenous soybean PP2C gene of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85 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 3097-3121; (ii) nucleotides 3296-3320; or (iii) nucleotides 3734-3758; all of the PP2C gene of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85.

[0084] 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 PP2C protein while removing at least one, two, three codons, thus resulting in a mutant PP2C protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the PP2C 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 PP2C gene. In certain embodiments, the at least one mutation of the PP2C 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, or 180 nucleotides in a protein coding region of an exon of SEQ ID NO: 85 or at an equivalent position in an allelic variant of SEQ ID NO: 85 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 3097-3121, 3296- 3320, or 3734-3758 of SEQ ID NO: 85 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: (i) amino acids 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, and / or 138; (ii) amino acids 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, and / or 161; and / or (iii) amino acids 197, 198, 199, 200, 201, 202. 203. 204, 205. 206, 207, 208, 209, 210, 211, and / or 212; all of SEQ ID NO: 87, or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0085] The target endogenous soybean transcription factor RNA Processing Factor 1 (RPF1) gene comprises the genomic DNA of SEQ ID NO: 98 (depicted in Figure 9A-F), SEQ ID NO: 14 (a shortened version of SEQ ID NO: 98), and allelic variants thereof located on soybean chromosome 8. The endogenous soybean RPF1 gene is located at nucleotides 8326291-8330229 of chromosome 8 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.08G108400 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). Allelic variants of an endogenous soybean RPF1 gene include variants which encode RPF1 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: 100. Allelic variants of an endogenous soybean RPF1 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: 98, 104, or 111. In certain embodiments, allelic variants of the endogenous soybean RPF1 gene are isomorphic alleles of the endogenous soybean RPF1 gene. RPF1 gene transcripts comprising distinct 3’ UTRs are disclosed herein(SEQ ID NO: 107) and in sequence databases (Glyma.08G108400.1 (SEQ ID NO: 108, 109, and 110) and Glyma.08G108400.2 (SEQ ID NO: 113 and 114). All RPF1 gene transcripts comprise a single exon which contains the open reading frame (ORF) encoding the RFP1 protein. Guide RNAs comprising the spacers encoded by SEQ ID NO: 101, 102, and 103 are used in conjunction with suitable Cas nucleases to introduce amorphic or hypomorphic mutations in the single exon which contains the open reading frame (ORF) encoding the RFP1 protein.

[0086] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean RPF1 gene of SEQ ID NO: 98, 104, 111, 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 of the RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous RPF1 gene. The insertion, deletion, and / or substitution can be made anywhere in the RPF1 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 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, or 3939 nucleotides) of the RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an 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 120-1955 of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98) of the RPF1 gene. In certain embodiments, the at least one mutation in the RPF1 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 RPF1 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) an N-terminal RPF1 protein coding region (e g., nucleotides 120- 1955 of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98) or in an equivalent position of an allelic variant of SEQ ID NO: 98). 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, 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, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides)corresponding to nucleotides 120-1955 (z.e., within the protein and intron coding region) of the RPF1 gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98. 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 415-439; (ii) nucleotides 675-699; or (iii) nucleotides 770-794; all of the RPF1 gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98.

[0087] 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 RPF1 gene. In certain embodiments, mutations of the RPF1 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in the exon of the RPF1 gene (e.g., the exon located between nucleotides 120- 1955 of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98). In certain embodiments, mutations of the RPF1 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, 374, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580, 581, 583, 584, 586, 587, 589, 590, 592,593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608, 610, 611, 613, 614, 616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637, 638, 640, 641, 643, 644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665, 667, 668, 670, 671, 673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703, 704, 706, 707, 709, 710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731, 733, 734, 736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760, 761, 763, 764, 766, 767, 769, 770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788, 790, 791, 793, 794, 796, 797, 799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817, 818, 820, 821, 823, 824, 846, 847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, 845, 847, 848, 850, 851, 853, 854, 856, 857, 859, 860, 862, 863, 865, 866, 868, 869, 871, 872, 874, 875, 877, 878, 880, 881, 883, 884, 886, 887, 889, 890, 892, 893, 895, 896, 898, 899, 901, 902, 904, 905, 907, 908, 910, 911, 913, 914, 916, 917, 919, 920, 922, 923, 925, 926, 928, 929, 931, 932, 934, 935, 937, 938, 940, 941, 943, 944, 946, 947, 949, 950, 952, 953, 955, 956, 958, 959, 961, 962, 964, 965, 967, 968, 970, 971, 973, 974, 976, 977, 979, 980, 982, 983, 985, 986, 988, 989, 991, 992, 994, 995, 997, 998, 1000, 1001, 1003, 1004, 1006, 1007, 1009, 1010, 1012, 1013, 1015, 1016, 1018, 1019, 1021, 1022, 1024, 1025, 1027, 1028, 1030, 1031, 1033, 1034, 1036, 1037, 1039, 1040, 1042, 1043, 1045, 1046, 1048, 1049, 1051, 1052, 1054, 1055, 1057, 1058, 1060, 1061, 1063, 1064, 1066, 1067, 1069, 1070, 1072, 1073, 1075, 1076, 1078, 1079, 1081, 1082, 1084, 1085, 1087, 1088, 1090, 1091, 1093, 1094, 1096, 1097, 1099, 1100, 1102, 1103, 1105, 1106, 1108, 1109, 1111, 1112, 1114, 1115, 1117, 1118, 1120, 1121, 1123, 1124, 1126, 1127, 1129, 1130, 1132, 1133, 1135, 1136, 1138, 1139, 1141, 1142, 1144, 1145, 1147, 1148, 1150, 1151, 1153, 1154, 1156, 1157, 1159, 1160, 1162, 1163, 1165, 1166, 1168, 1169, 1171, 1172, 1174, 1175, 1177, 1178, 1180, 1181, 1183, 1184, 1186, 1187, 1189, 1190, 1192, 1193, 1195, 1196, 1198, 1199, 1201, 1202, 1204, 1205, 1207, 1208, 1210, 1211, 1213, 1214, 1216, 1217, 1219, 1220, 1222, 1223, 1225, 1226, 1228, 1229, 1231, 1232, 1234, 1235, 1237, 1238, 1240, 1241, 1243, 1244, 1246, 1247, 1249, 1250, 1252, 1253, 1255, 1256, 1258, 1259, 1261, 1262, 1264, 1265, 1267, 1268, 1270, 1271, 1273, 1274, 1276, 1277, 1279, 1280, 1282, 1283, 1285, 1286, 1288, 1289, 1291, 1292, 1294, 1295, 1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1309, 1310, 1312, 1313, 1315, 1316, 1318, 1319, 1321, 1322, 1324, 1325, 1327, 1328, 1330, 1331, 1333, 1334, 1336, 1337, 1339, 1340, 1342, 1343, 1345, 1346, 1348, 1349, 1351, 1352, 1354, 1355, 1357, 1358, 1360, 1361, 1363, 1364, 1366, 1367, 1369, 1370, 1372, 1373, 1375, 1376, 1378, 1379, 1381, 1382, 1384, 1385, 1387, 1388, 1390, 1391, 1393, 1394, 1396, 1397, 1399, 1400, 1402, 1403, 1405, 1406, 1408, 1409, 1411, 1412, 1414, 1415, 1417, 1418, 1420, 1421, 1423, 1424, 1426, 1427, 1429, 1430, 1432, 1433, 1435, 1436, 1438, 1439, 1441, 1442, 1444, 1445, 1447, 1448, 1450, 1451, 1453, 1454, 1456, 1457, 1459, 1460, 1462, 1463, 1465, 1466, 1468, 1469, 1471, 1472,1474, 1475, 1477, 1478, 1480, 1481, 1483, 1484, 1486, 1487, 1489, 1490, 1492, 1493, 1495, 1496, 1498, 1499, 1501, 1502, 1504, 1505, 1507, 1508, 1510, 1511, 1513, 1514, 1516, 1517, 1519, 1520, 1522, 1523, 1525, 1526, 1528, 1529, 1531, 1532, 1534, 1535, 1537, 1538, 1540,1541, 1543, 1544, 1546, 1547, 1549, 1550, 1552, 1553, 1555, 1556, 1558, 1559, 1561, 1562,1564, 1565, 1567, 1568, 1570, 1571, 1573, 1574, 1576, 1577, 1579, 1580, 1582, 1583, 1585,1586, 1588, 1589, 1591, 1592, 1594, 1595, 1597, 1598, 1600, 1601, 1603, 1604, 1606, 1607,1609, 1610, 1612, 1613, 1615, 1616, 1618, 1619, 1621, 1622, 1624, 1625, 1627, 1628, 1630,1631, 1633, 1634, 1636, 1637, 1639, 1640, 1642, 1643, 1645, 1646, 1648, 1649, 1651, 1652,1654, 1655, 1657, 1658, 1660, 1661, 1663, 1664, 1666, 1667, 1669, 1670, 1672, 1673, 1675,1676, 1678, 1679, 1681, 1682, 1684, 1685, 1687, 1688, 1690, 1691, 1693, 1694, 1696, 1697,1699, 1700, 1702, 1703, 1705, 1706, 1708, 1709, 1711, 1712, 1714, 1715, 1717, 1718, 1720,1721, 1723, 1724, 1726, 1727, 1729, 1730, 1732, 1733, 1735, 1736, 1738, 1739, 1741, 1742,1744, 1745, 1747, 1748, 1750, 1751, 1753, 1754, 1756, 1757, 1759, 1769, 1771, 1772, 1774,1775, 1777, 1778, 1780, 1781, 1783, 1784, 1786, 1787, 1789, 1790, 1792, 1793, 1795, 1796,1798, 1799, 1801, 1802, 1804, 1805, 1807, 1808, 1810, 1811, 1813, 1814, 1816, 1817, 1819, 1820, 1822, 1823, 1825, 1826, 1828, 1829, 1831, 1832, 1834, or 1836 nucleotides of the exon located in the endogenous soybean RPF1 gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98 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 415-439; (ii) nucleotides 675-699; or (iii) nucleotides 770-794; all of the RPF1 gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98.

[0088] 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 RPF1 protein while removing at least one, two, three codons, thus resulting in a mutant RPF1 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the RPF1 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 RPF1 gene. In certain embodiments, the at least one mutation of the RPF1 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, 552,555, 558, 561, 564, 567, 570, 573, 576, 579, 582, 585, 588, 591, 594, 597, 600, 603, 606, 609,612, 615, 618, 621, 624, 627, 630, 633, 636, 639, 642, 645, 648, 651, 654, 657, 660, 663, 666,669, 672, 675, 678, 681, 684, 687, 690, 693, 696, 699, 702, 705, 708, 711, 714, 717, 720, 723,726, 729, 732, 735, 738, 741, 744, 747, 750, 753, 756, 759, 762, 765, 768, 771, 774, 777, 780,783, 786, 789, 792, 795, 798, 801, 804, 807, 810, 813, 816, 819, 822, 825, 828, 831, 834, 837,840, 843, 846, 849, 852, 855, 858, 861, 864, 867, 870, 873, 876, 879, 882, 885, 888, 891, 894,897, 900, 903, 906, 909, 912, 915, 918, 921, 924, 927, 930, 933, 936, 939, 942, 945, 948, 951,954, 957, 960, 963, 966, 969, 972, 975, 978, 981, 984, 987, 990, 993, 996, 999, 1002, 1005, 1008, 1011, 1014, 1017, 1020, 1023, 1026, 1029, 1032, 1035, 1038, 1041, 1044, 1047, 1050,1053, 1056, 1059, 1062, 1065, 1068, 1071, 1074, 1077, 1080, 1083, 1086, 1089, 1092, 1095,1098, 1101, 1104, 1107, 1110, 1113, 1116, 1119, 1122, 1125, 1128, 1131, 1134, 1137, 1140,1143, 1146, 1149, 1152, 1155, 1158, 1161, 1164, 1167, 1170, 1173, 1176, 1179, 1182, 1185,1188, 1191, 1194, 1197, 1200, 1203, 1206, 1209, 1212, 1215, 1218, 1221, 1224, 1227, 1230,1233, 1236, 1239, 1242, 1245, 1248, 1251, 1254, 1257, 1260, 1263, 1266, 1269, 1272, 1275,1278, 1281, 1284, 1287, 1290, 1293, 1296, 1299, 1302, 1305, 1308, 1311, 1314, 1317, 1320,1323, 1326, 1329, 1332, 1335, 1338, 1341, 1344, 1347, 1350, 1353, 1356, 1359, 1362, 1365,1368, 1371, 1374, 1377, 1380, 1383, 1386, 1389, 1392, 1395, 1398, 1401, 1404, 1407, 1410,1413, 1416, 1419, 1422, 1425, 1428, 1431, 1434, 1437, 1440, 1443, 1446, 1449, 1452, 1455,1458, 1461, 1464, 1467, 1470, 1473, 1476, 1479, 1482, 1485, 1488, 1491, 1494, 1497, 1500,1503, 1506, 1509, 1512, 1515, 1518, 1521, 1524, 1527, 1530, 1533, 1536, 1539, 1542, 1545,1548, 1551, 1554, 1557, 1560, 1563, 1566, 1569, 1572, 1575, 1578, 1581, 1584, 1587, 1590,1593, 1596, 1599, 1602, 1605, 1608, 1611, 1614, 1617, 1620, 1623, 1626, 1629, 1632, 1635,1638, 1641, 1644, 1647, 1650, 1653, 1656, 1659, 1662, 1665, 1668, 1671, 1674, 1677, 1680,1683, 1686, 1689, 1692, 1695, 1698, 1701, 1704, 1707, 1710, 1713, 1716, 1719, 1722, 1725,1728, 1731, 1734, 1737, 1740, 1743, 1746, 1749, 1752, 1755, 1758, 1761, 1764, 1767, 1770,1773, 1776, 1779, 1782, 1785, 1788, 1791, 1794, 1797, 1800, 1803, 1806, 1809, 1812, 1815,1818, 1821, 1824, 1827, 1830, 1833, 1836 in a protein coding region of an exon of SEQ ID NO: 98 or at an equivalent position in an allelic variant of SEQ ID NO: 98 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 415-439, 675-699, or 770-794 of SEQ ID NO: 98 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 nucleotidesencoding one or more amino acids corresponding to: (i) amino acids 96, 97, 98, 99, 100, 101,102, 103, 104, 105, 106, 107, 108, 109, and / or 110; (ii) amino acids 182, 183, 184, 185, 186,187, 188, 189, 190, 191, 192, 193, 194, 195, 196, and / or 197; and / or (iii) amino acids 214, 215,216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, and / or 229; all of SEQ ID NO:100 or an allelic variant thereof, wherein the deletion preserves the reading frame.

[0089] The target endogenous soybean transcription factor TCP5-like (TCP5) gene comprises the genomic DNA of SEQ ID NO: 115 and allelic variants thereof located on soybean chromosome 4. The endogenous soybean TCP5 gene is located at nucleotides 38,837,566 to 38,842,283 of chromosome 4 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.04gl61400 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). Allelic variants of an endogenous soybean TCP5 gene include variants which encode TCP5 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: 117. Allelic variants of an endogenous soybean TCP5 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: 115. In certain embodiments, allelic variants of the endogenous soybean TCP5 gene are isomorphic alleles of the endogenous soybean TCP5 gene. The wild-type soybean transcription factor TCP5-like (TCP5) gene encodes a member of the teosinte branchedl, cycloidea, and proliferating cell (TCP) transcription factor family. TCP5 and other members of TCP gene family which contain basic-Helix-Loop-Helix (bHLH) and R motifs.

[0090] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean TCP5 gene of SEQ ID NO: 115, 121, 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 of the TCP5 gene of SEQ ID NO: 115, 116, 212, 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 TCP5 gene. The insertion, deletion, and / or substitution can be made anywhere in the TCP5 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, or 4718 nucleotides) of the TCP5 gene of SEQ ID NO: 115, 116, 121, or allelic variant thereof. Incertain 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 1412-2575 of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115) of the TCP5 gene. In certain embodiments, the at least one mutation in the TCP5 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 TCP5 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of exon 1 (z.e., nucleotides 1412-2575 of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115) or in an equivalent position of an allelic variant of SEQ ID NO: 115). 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, 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, or 1164 nucleotides) corresponding to nucleotides 1412-2575 (z.e., within the first exon) of the TCP5 gene of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115). 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 1628, 1633, 1638, 1643, or 1648 to 1652, 1657, 1662, 1667, or 1672; (ii) nucleotides 1525, 1530, 1535, 1540, or 1545 to 1549, 1554, 1559, 1564, or 1569; or (iii) nucleotides 1769, 1774, 1779. 1784, or 1789 to 1793, 1798, 1803, 1808, or 1813 ofthe TCP5 gene of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115.

[0091] 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 TCP5 gene. In certain embodiments, mutations of the TCP5 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the TCP5 gene. In certain embodiments, mutations of the TCP5 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, 209,11, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 39, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 68, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 96, 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, 374, 376, 377, 379, 380,382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400, 401, 403, 404, 406, 407, 409, 10, 412, 413, 415, 416, 418, 419, 421, 422, 424, 425, 427, 428, 430, 431, 433, 434, 436, 437, 39, 440, 442, 443, 445, 446, 448, 449, 451, 452, 454, 455, 457, 458, 460, 461, 463, 464, 466, 67, 469, 470, 472, 473, 475, 476, 478, 479, 481, 482, 484, 485, 487, 488, 490, 491, 493, 494, 96, 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, 554, 556, 557, 559, 560, 562, 563, 565, 566, 568, 569, 571, 572, 574, 575, 577, 578, 580,581, 583, 584, 586, 587, 589, 590, 592, 593, 595, 596, 598, 599, 601, 602, 604, 605, 607, 608,610, 611, 613, 614, 616, 617, 619, 620, 622, 623, 625, 626, 628, 629, 631, 632, 634, 635, 637,638, 640, 641, 643, 644, 646, 647, 649, 650, 652, 653, 655, 656, 658, 659, 661, 662, 664, 665,667, 668, 670, 671, 673, 674, 676, 677, 679, 680, 682, 683, 685, 686, 688, 689, 700, 701, 703,704, 706, 707, 709, 710, 712, 713, 715, 716, 718, 719, 721, 722, 724, 725, 727, 728, 730, 731, 733, 734, 736, 737, 739, 740, 742, 743, 745, 746, 748, 749, 751, 752, 754, 755, 757, 758, 760,761, 763, 764, 766, 767, 769, 770, 772, 773, 775, 776, 778, 779, 781, 782, 784, 785, 787, 788,790, 791, 793, 794, 796, 797, 799, 800, 802, 803, 805, 806, 808, 809, 811, 812, 814, 815, 817,818, 820, 821, 823, 824, 846, 847, 829, 830, 832, 833, 835, 836, 838, 389, 841, 842, 844, 845,847, 848, 850, 851, 853, 854, 856, 857, 859, 860, 862, 863, 865, 866, 868, 869, 871, 872, 874,875, 877, 878, 880, 881, 883, 884, 886, 887, 889, 890, 892, 893, 895, 896, 898, 899, 901, 902,904, 905, 907, 908, 910, 911, 913, 914, 916, 917, 919, 920, 922, 923, 925, 926, 928, 929, 931,932, 934, 935, 937, 938, 940, 941, 943, 944, 946, 947, 949, 950, 952, 953, 955, 956, 958, 959,961, 962, 964, 965, 967, 968, 970, 971,973, 974, 976, 977, 979, 980, 982, 983, 985, 986, 988, 989, 991, 992, 994, 995, 997, 998, 1000, 1001, 1003, 1004, 1006, 1007, 1009, 1010, 1012, 1013, 1015, 1016, 1018, 1019, 1021, 1022, 1024, 1025, 1027, 1028, 1030, 1031, 1033, 1034, 1036,1037, 1039, 1040, 1042, 1043, 1045, 1046, 1048, 1049, 1051, 1052, 1054, 1055, 1057, 1058,1060, 1061, 1063, 1064, 1066, 1067, 1069, 1070, 1072, 1073, 1075, 1076, 1078, 1079, 1081,1082, 1084, 1085, 1087, 1088, 1090, 1091, 1093, 1094, 1096, 1097, 1099, 1100, 1102, 1103,1005, 1106, 1108, 1109, 1111, 1112, 1114, 1115, 1117, 1118, 1120, 1121, 1123, 1124, 1126,1127, 1129, 1130, 1132, 1133, 1135, 1136, 1138, 1139, 1141, 1142, 1144, 1145, 1147, 1148.1150. 1151, 1153, 1154, 1156, 1157, 1159, 1160, 1162, and 1163 nucleotides of the endogenoussoybean TCP5 gene of SEQ ID NO: 115 located at nucleotides 1412-2575 (z.e., within the first exon) of SEQ ID NO: 115 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 1628, 1633, 1638, 1643, or 1648 to 1652, 1657, 1662, 1667, or 1672; (ii) nucleotides 1525, 1530, 1535, 1540, or 1545 to 1549, 1554, 1559, 1564, or 1569 ; or (iii) nucleotides 1769, 1774, 1779. 1784, or 1789 to 1793, 1798, 1803, 1808, or 1813 of the TCP5 gene of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115.

[0092] 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 TCP5 protein while removing at least one, two, three codons, thus resulting in a mutant TCP5 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the TCP5 gene can comprise a deletion of any number of nucleotides that are divisible by 3 in an exon of the TCP5 gene. In certain embodiments, the at least one mutation of the TCP5 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, 555, 558, 561, 564,567, 570, 573, 576, 579, 582, 585, 588, 591, 594, 597, 600, 603, 606, 609, 612, 615, 618, 621,624, 627, 630, 633, 636, 639, 642, 645, 648, 651, 654, 657, 660, 663, 666, 669, 672, 675, 678,681, 684, 687, 690, 693, 696, 699, 702, 705, 708, 711, 714, 717, 720, 723, 726, 729, 732, 735,738, 741, 744, 747, 750, 753, 756, 759, 762, 765, 768, 771, 774, 777, 780, 783, 786, 789, 792,795, 798, 801, 804, 807, 810, 813, 816, 819, 822, 825, 828, 831, 834, 837, 840, 843, 846, 849,852, 855, 858, 861, 864, 867, 870, 873, 876, 879, 882, 885, 888, 891, 894, 897, 900, 903, 906,909, 912, 915, 918, 921, 924, 927, 930, 933, 936, 939, 942, 945, 948, 951, 954, 957, 960, 963,966, 969, 972, 975, 978, 981, 984, 987, 990, 993, 996, 999, 1002, 1005, 1008. 1011, 1114, 1017.1020, 1023, 1026, 1029, 1032, 1035, 1038, 1041, 1044, 1047, 1050, 1053, 1056, 1059, 1062,1065, 1068, 1071, 1074, 1077, 1080, 1083, 1086, 1089, 1092, 1095, 1098, 1101, 1104, 1107,1110, 1113, 1116, 1119, 1122, 1125, 1128, 1131, 1134, 1137, 1140, 1143, 1146, 1149, 1152,1155, 1158, 1161, and 1164 nucleotides of the endogenous soybean TCP5 gene of SEQ ID NO: 115 located at nucleotides 1412-2575 (z.e., within the first exon) of SEQ ID NO: 115 or at an equivalent position in an allelic variant of SEQ ID NO: 115 and preserve the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3 nucleotides corresponding to nucleotides 1628, 1633, 1638, 1643, or 1648 to 1652, 1657, 1662, 1667, or 1672 or nucleotides 1525, 1530, 1535, 1540, or 1545 to 1549, 1554, 1559, 1564, or 1569, or nucleotides 1769, 1774, 1779. 1784, or 1789 to 1793, 1798, 1803, 1808, or 1813 of SEQ ID NO: 115 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 73, 74, 75, 76, 77, 78, or 79 to 81, 82, 83, 84, 85, 86, or 87, or amino acids 39, 40, 41, 42, 43, 44, or 45 to 46, 47, 48, 49, 50, 51, or 52, or amino acids 120, 121, 122, 123, 124, 125, or 126 to 128, 129, 130, 131, 132, 133, or 134 of SEQ ID NO: 117 or an allelic variant thereof which preserves the reading frame.

[0093] In certain embodiments, 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is increased in comparison to the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of a wild-type or control soybean plant lacking the at least one amorphic or hypomorphic allele of the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is preserved or further enhanced when the at least one amorphic or hypomorphic allele of the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is combined with least one mutation in a distinct soybean gene (e.g., a hypomorphic or amorphic allele of a soybean AlPlOa, AlPlOb, BS1, BS2, FT la, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene).

[0094] In certain embodiments, the seeds per pod for the soybean plant comprising the at least one mutation e.g., loss-of-function mutation) in the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is increased in comparison to the seeds per pod for a wild-type or control soybean plant lacking the at least one mutation. Incertain 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 the CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 greater in comparison to the seeds per pod from the corresponding wildtype 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 CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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(s). In certain embodiments, the percentage of 3 seeded pods for the soybean plant comprising the at least one mutation in the CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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%.

[0095] In certain embodiments, the pod count per soybean plant comprising the at least one mutation (e.g., loss-of-function mutation) in the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is increased in comparison to the pod count perplant 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 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 loss-of-function mutation in CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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.

[0096] 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 (e.g., loss-of-function mutation) in the CRN, AMIN, A0C4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 plant 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 CRN, AML4, A0C4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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.

[0097] Soybean seed lots comprising the soybean seeds comprising the at least one mutation in CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are provided. In certain embodiments, soybean plants comprising the mutated CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene (e.g., a wild-type soybean plant homozygous for a wild-type CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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.

[0098] Also provided are polynucleotides comprising any of the aforementioned mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 genes or fragments thereof. In certain embodiments, polynucleotides comprising at least one mutation relative to the endogenous soybean CRN gene of SEQ ID NO: 1 or 7; AML4 gene of SEQ ID NO: 11; AOC4 gene of SEQ ID NO: 15 or 21; CYP76C-1 gene of SEQ ID NO: 25 or 31; CYP76C-2 gene of SEQ ID NO: 35 or 41; HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, or 70; KHZ1 gene of SEQ ID NO: 75 or 81; PP2C gene of SEQ ID NO: 85, 91, or 95; RPF1 gene of SEQ ID NO: 98 or 104; and / or TCP5 gene of SEQ ID NO: 115 or 121 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, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121 with the proviso that the sequences are not identical to across their entire length to SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121. In certain embodiments, the polynucleotide is an isolated polynucleotide.

[0099] A summary of the biological sequences described herein and provided herewith in the aforementioned sequence listings is set forth in Table 1.

[0100] Table 1 Summary of Biological Sequences

[0101] 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.

[0102] 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.

[0103] This disclosure is also directed to methods for producing a soybean plant having at least one mutation in the endogenous soybean CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene by crossing a first parent soybean plant with a second parent soybean plant wherein the first or second parent soybean plant comprises the at least one mutation. Further, both the first and second parent soybean plants can comprise the at least one mutation. Any such methods using a soybean plant comprising the at least one mutation are part of this disclosure: selfing, backcrosses, 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 for 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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.

[0104] Field crops are bred through techniques that take advantage of the plant’s method of pollination. A soybean plant of the disclosure can be self-pollinated, sib-pollinated, or cross pollinated to create a pedigree soybean plant. A plant is self-pollinated if pollen from one flower is transferred to the same or another flower of the same plant. A plant is sib-pollinated when individuals within the same family or variety are used for pollination. A plant is cross-pollinated if the pollen comes from a flower on a different plant from a different family or variety. The terms “cross-pollination” and “out-cross” as used herein do not include self-pollination or sib- pollination. Soybean plants (Glycine max) are recognized to be naturally self-pollinated plants which, while capable of undergoing cross-pollination, rarely do so in nature. Insects are reported by some researchers to carry pollen from one soybean plant to another and it generally is estimated that less than one percent of soybean seed formed in an open planting can be traced to cross-pollination, z.e., less than one percent of soybean seed formed in an open planting is capable of producing Fi hybrid soybean plants.

[0105] 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.

[0106] In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising at least one mutation (e.g., a loss-of-function mutation) in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof, PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof; and a transgenic locus are provided. In certain embodiment, the at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof is combined with one or more soybean GM events providing tolerance to any one or a combination of glyphosate-based, glufosinatebased, HPPD inhibitor-based, sulfonylurea- or imidazolinone-based, AHAS- or ALS-inhibiting and / or auxin-type (e.g., dicamba, 2,4-D) herbicides and / or an insect resistance trait. GM events that can be combined with the mutations disclosed herein include Event EE-GM3 (aka FG-072, MST-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 (dicamba- tolerant 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 inWO20 10 / 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-87708-9xMON-89788-l), Event HOS*Event 40-3-2 (aka Plenish High OleicSoybeans 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- 877Ol-2xMON-89788-l), DAS-81419-2xDAS-44406-6 (aka Conkesta™ Enlist E3™ Soybean, DAS-81419-2xDAS-444O6-6), Event DAS-68416-4 xEvent MON 89788 (aka Enlist™ RoundUp Ready® 2 Soybean, DAS-68416-4xMON-89788-l), Event MON-87769-7xEvent MON-89788-1 (aka Omega-3 x Genuity Roundup Ready 2 Yield Soybeans), Event MON 87705xEvent MON 89788 (aka Vistive Gold, MON-87705-6xMON-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 CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof include those set forth in Table 1. Also provided herein are soybean plant cells, plant parts (e.g., seeds), and plants comprising at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO:85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof 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 and US20230250441; and U.S. Patent No.11,242,534, which are each incorporated herein by reference in their entireties.

[0107] Table 2. Transgenic Soybean Events

[0108] In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising the at least one mutation (e.g., a loss-of-function mutation) in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof and at least one mutation (e.g., a loss-of-function 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene of the disclosure include mutations in any one or a combination of the soybean AlPlOa, AlPlOb, BS1, BS2, FTla, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is combined with a mutation in the soybean BS1 gene. 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, theat least one mutation in the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is combined with a mutation in the soybean BS2 gene. 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is combined with a mutation in the soybean FTla gene. The FTla gene (Glyma.18G298900) 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 CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof is combined with a mutation in the soybean JAG1 gene. The JAG1 gene is located at nucleotides 35827671 to 35830107 of chromosome 20 of the Glycine max Wm82.a2.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof, HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof is combined with a mutation in the soybean JAG2 gene. The JAG2 gene is located at nucleotides 49718688 to 49722581 of chromosome 10 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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. In certain embodiments, the at least one mutation in the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C,RPF1, and / or TCP5 gene 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.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean CRN, AMIN, A0C4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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. In certain embodiments, the at least one mutation in the endogenous soybean CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene is combined with a mutation (e.g., a deletion) in the TFLlb gene (Glyma. l9gl94300) which can be a promoter element deletion as described in WO2023086765, which is incorporated herein by reference in its entirety.

[0109] Methods of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising an amorphic or hypomorphic allele of a CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 or hypomorphic allele of a CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are provided. 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).

[0110] 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.

[0111] The disclosure also provides a method of making a soybean plant comprising an amorphic or hypomorphic allele of a CRN, AMIN, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene. 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene (e.g., in the promoter, 5’ UTR, exon(s), intron(s), and / or 3’ UTR of thegene, including such genes, promoters, 5’ UTR, exon(s), intron(s), and / or 3’ UTR elements provided in Table 1 or allelic variants thereof). Hypomorphic alleles of the CRN, AML4, A0C4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 those genes. 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 CRN gene (e.g., SEQ ID NO: 1, 7, or an allelic variant thereof), AML4 gene (e.g., SEQ ID NO: 11 or an allelic variant thereof), AOC4 gene (e.g., SEQ ID NO: 15, 21, or an allelic variant thereof), CYP76C-1 gene (e.g., SEQ ID NO: 25, 31, or an allelic variant thereof), CYP76C-2 gene e.g., SEQ ID NO: 35, 41, or an allelic variant thereof), HB-1 gene (e.g., SEQ ID NO: 45, 51, 55, 60, 65, or 70, or an allelic variant thereof), KHZ1 gene (e.g., SEQ ID NO: 75, 81, or an allelic variant thereof), PP2C gene (e.g., SEQ ID NO: 85, 91, 95, or an allelic variant thereof), RPF1 gene (e.g., SEQ ID NO: 98, 104, 111, or an allelic variant thereof), and / or TCP5 gene (e.g., SEQ ID NO: 115, 121, 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 CRN gene (e.g., SEQ ID NO: 1, 7 or an allelic variant thereof), AML4 gene (e.g., SEQ ID NO: 11 or an allelic variant thereof), AOC4 gene (e.g., SEQ ID NO: 15, 21, or an allelic variant thereof), CYP76C-1 gene (e.g., SEQ ID NO: 25, 31, or an allelic variant thereof), CYP76C-2 gene (e.g., SEQ ID NO: 35, 41 or an allelic variant thereof), HB-1 gene (e.g., SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof), KHZ1 gene (e.g., SEQ ID NO: 75, 81 or an allelic variant thereof), PP2C gene (e.g., SEQ ID NO: 85, 91, 95, or an allelic variant thereof), RPF1 gene (e.g., SEQ ID NO: 98, 104, 111, or an allelic variant thereof), and / or TCP5 gene (e.g., SEQ ID NO: 115, 121, or an allelic variant thereof), followed by homology-directed repair (HDR), microhomology-mediated end joining (MMEJ), or NHEJ to introduce a desired donor or other DNA template polynucleotide at the DSB, followed by recovery of the desired mutation. Examples of such gene editing molecules include: (a) a nuclease comprising an RNA- guided nuclease, an RNA-guided DNA endonuclease or RNA directed DNA endonuclease (RdDe), a class 1 CRISPR type nuclease system, a class 2 type II Cas nuclease, a Cas9, a nCas9 nickase, a class 2 type V Cas nuclease, a 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, a codon-optimized nuclease, a zinc-finger nuclease (ZFN) or nickase, atranscription activator-like effector nuclease (TAL-effector nuclease or TALEN) or nickase (TALE-nickase), an Argonaute, and a meganuclease or engineered meganuclease; (b) a polynucleotide encoding one or more nucleases capable of effectuating site-specific alteration (including introduction of a DSB or SSB) of a target nucleotide sequence; (c) a guide RNA (gRNA) for use with an RNA-guided nuclease, or a DNA encoding a gRNA for use with an RNA-guided nuclease; (d) optionally donor DNA template polynucleotides suitable for insertion at a break in genomic DNA by homology-directed repair (HDR) or microhomology-mediated end joining (MMEJ); and (e) optionally other DNA templates (e.g., dsDNA, ssDNA, or combinations thereof) suitable 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.

[0112] In certain embodiments, the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB- 1, KHZ1, PP2C, RPF1, and / or TCP5 gene and plant cells, parts including seeds, and plants comprising the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 / 0I8104 (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 / 0082478 Al 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-end cutting RNA-guided endonucleases include Cast 2a, Cast 2b, Casl2d, Casl 2e, and Casl2i.

[0113] Guide RNA molecules comprising a spacer RNA molecule which targets the CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof are provided. In certain embodiments, thespacer RNA molecule targets a portion of the first exon (z.e., nucleotides 988-1901 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) of the CRN 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: 4, 5, or 6. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 4, 5, or 6, can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated CRN 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, or 3141 nucleotides) of the CRN 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 or 914 nucleotides) corresponding to nucleotides 988-1901 of the CRN 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 nucleotides 1215, 1220, 1225, 1230, or 1235 to 1239, 1244, 1249, 1254, or 1259 or nucleotides 1238, 1243, 1248, 1253, or 1258 to 1262, 1267, 1272, 1277, or 1282, or nucleotides 1801, 1806, 1811, 1816, or 1821 to 1825, 1830, 1835, 1840, or 1845 ofthe CRN gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1.

[0114] Guide RNA molecules comprising a spacer RNA molecule which targets the AML4 gene of SEQ ID NO: 11, or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the fifth exon (z.e., nucleotides 2458 to 2928 of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11) of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 14. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 14 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g, the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated AML4 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, 6000, 6500, or 6959 nucleotides) of the AML4 gene of SEQ ID NO: 11 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, or 471 nucleotides) corresponding to nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11; 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 nucleotides 2604, 2609, 2614, 2619, or 2624 to 2628, 2633, 2638, 2643, or 2648 of the AML4 gene of SEQ ID NO: 11 or in an equivalent position of an allelic variant of SEQ ID NO: 11.

[0115] Guide RNA molecules comprising a spacer RNA molecule which targets the AOC4 gene of SEQ ID NO: 15, 21, 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 342-591, 695-816, and 1254-1655 of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 15) of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 18, 19, or 20. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 18, 19, or 20 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated AOC4 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, or 1873 nucleotides) of the AOC4 gene of SEQ ID NO: 15, 21, or an 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, or 402 nucleotides) corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 11; 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 337-361; (ii) nucleotides 382-406; and / or (iii) nucleotides 418-442; all in a A0C4 gene of SEQ ID NO: 15 or in an equivalent position of an allelic variant of SEQ ID NO: 11.

[0116] Guide RNA molecules comprising a spacer RNA molecule which targets the CYP76C-1 gene of SEQ ID NO: 25, 31, 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 142-1044 and 1199-1828 of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25) of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 28, 29, or 30. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 28, 29, or 30 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated CYP76C- 1 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, or 2216 nucleotides) of the CYP76C-1 gene of SEQ ID NO: 25, 31, or an 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, or 903 nucleotides) corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25; 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 294-318; (ii) nucleotides 453-477; and / or (iii) nucleotides 557-581; all in a CYP76C-1 gene of SEQ ID NO: 25 or in an equivalent position of an allelic variant of SEQ ID NO: 25.

[0117] Guide RNA molecules comprising a spacer RNA molecule which targets the CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the protein and intron coding region (i.e., nucleotides 60-2082 of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35) of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 38, 39, or 40. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 38, 39, or 40 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., theCasl2i3 nuclease of SEQ ID NO: 127) to generate mutated CYP76C-2 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, or 2398 nucleotides) of the CYP76C-2 gene of SEQ ID NO: 35 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, or 611 nucleotides) corresponding to nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35; 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 149-173; (ii) nucleotides 239-263; and / or (iii) nucleotides 292-316; all in a CYP76C-2 gene of SEQ ID NO: 35 or in an equivalent position of an allelic variant of SEQ ID NO: 35.

[0118] Guide RNA molecules comprising a spacer RNA molecule which targets the HB-1 gene of SEQ ID NO: 45, 51, or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the protein and intron coding region (i.e., nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45) of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 48, 49, or 50. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 48, 49, or 50 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated HB-1 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, 2250, 2500, 2750, 3000, 3250, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10070 nucleotides) of the HB-1 gene of SEQ ID NO: 45, 53, 55, 60, 65, 70, or an 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, or 846 nucleotides) corresponding to nucleotides 790- 985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635- 4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280- 8543, and 8836-9681 of the HB-1 gene of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45; 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 2720-2744; (ii) nucleotides 2809-2833; and / or (iii) nucleotides 2955-2979; all in a HB-1 gene of SEQ ID NO: 45 or in an equivalent position of an allelic variant of SEQ ID NO: 45.

[0119] Guide RNA molecules comprising a spacer RNA molecule which targets the KHZ1 gene of SEQ ID NO: 75, 81, 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 205-274, 684-744, and 3855-4617 of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75) of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 78, 79, or 80. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 78, 79, or 80 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated KHZ1 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, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, or 4769 nucleotides) of the KHZ1 gene of SEQ ID NO: 75, 81, or an 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, or 763 nucleotides) corresponding to nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75; 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 230-254; (ii) nucleotides 715-739; and / or(iii) nucleotides 3943-3967; all in a KHZ1 gene of SEQ ID NO: 75 or in an equivalent position of an allelic variant of SEQ ID NO: 75.

[0120] Guide RNA molecules comprising a spacer RNA molecule which targets the PP2C gene of SEQ ID NO: 85, 91, 95, 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 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85) of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 88, 89, or 90. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 88, 89, or 90 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated PP2C 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, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000, 5250, 5500, 5750, or 6059 nucleotides) of the PP2C gene of SEQ ID NO: 85, 91, or an 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, or 182 nucleotides) corresponding to nucleotides 73-254, 2058-2200, 3043- 3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 ofthe PP2C gene of SEQ ID NO: 85 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 3097-3121; (ii) nucleotides 3296-3320; and / or (iii) nucleotides 3734-3758; all in a PP2C gene of SEQ ID NO: 85 or in an equivalent position of an allelic variant of SEQ ID NO: 85.

[0121] Guide RNA molecules comprising a spacer RNA molecule which targets the RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the protein and intron coding region (i.e., nucleotides 120-1955 of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98) of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 101, 102, or 103. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 101, 102, or103 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated RPF1 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, 2250, 2500, 2750, 3000, 3250, 3500, or 3939 nucleotides) of the RPF1 gene of SEQ ID NO: 98 or an 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, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides) corresponding to nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98; 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 415-439; (ii) nucleotides 675-699; and / or (iii) nucleotides 770-794; all in a RPFl gene of SEQ ID NO: 98 or in an equivalent position of an allelic variant of SEQ ID NO: 98.

[0122] Guide RNA molecules comprising a spacer RNA molecule which targets the TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the first exon (i.e., nucleotides 1412-2575 of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115) of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 118. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 118 can be fused to a crRNA (DR) and used in conjunction with a Casl2a or Casl2i nuclease (e.g., the Casl2i3 nuclease of SEQ ID NO: 127) to generate mutated TCP5 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, or 4718 nucleotides) of the TCP5 gene of SEQ ID NO: 115 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, or 1164 nucleotides) corresponding to nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115; 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 nucleotides 1628, 1633, 1638, 1643, or 1648 to 1652, 1657, 1662, 1667, or 1672 or nucleotides 1525, 1530, 1535, 1540, or 1545 to 1549, 1554, 1559, 1564, or 1569 , or nucleotides 1769, 1774, 1779. 1784, or 1789 to 1793, 1798, 1803, 1808, or 1813 of the TCP5 gene of SEQ ID NO: 115 or in an equivalent position of an allelic variant of SEQ ID NO: 115.

[0123] 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 for design of crRNAs or sgRNAs used with Casl2a proteins. In some instances, Casl2a 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.

[0124] 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.

[0125] 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.

[0126] The nuclease efficiency and occurrence of off-target activity for a given gRNA / endonuclease combination can be influenced by a number of factors including similarities and dissimilarities between the target site and various off-target sites, as well as the particular endonuclease used. For example, the ability of a given gRNA to promote cleavage at a target sequence in a genomic DNA molecule may relate to the accessibility of the target sequence, which depends on one or more factors that include the chromatin structure of the genomic DNA molecule and / or proximity to transcription factor binding sites. For example, target sequences located within a region of the genomic DNA molecule having a high condensed chromatin structure are less accessible than target sequences located within a region of the genomic DNA molecule having an open chromatin structure. As a further example, target sequences proximal to a region of the genomic DNA molecule bound by a transcription factor or other regulatory protein may be less accessible than target sequences proximal to a region of the genomic DNA molecule that is unbound by regulatory proteins. Moreover, the cell state andtype of cell may influence the accessibility of target sequences, for example, by influencing the chromatin structure of genomic DNA.

[0127] In certain embodiments, the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB- 1, KHZ1, PP2C, RPF1, and / or TCP5 gene and plant cells, parts including seeds, and plants comprising the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 (Urnov et al. (2010) Nature Rev. Genet., 11 :636 - 646; Mohanta et al. (2017) Genes vol. 8,12: 399; Ramirez et al. Nucleic Acids Res. (2012); 40(12): 5560-5568; Liu et al. (2013) Nature Communications, 4: 2565) can be adapted for use in the methods set forth herein. The zinc finger binding domains of the zinc finger nuclease or nickase provide specificity and can be engineered to specifically recognize any desired target DNA sequence. The zinc finger DNA binding domains are derived from the DNA-binding domain of a large class of eukaryotic transcription factors called zinc finger proteins (ZFPs). The DNA-binding domain of ZFPs typically contains a tandem array of at least three zinc “fingers” each recognizing a specific triplet of DNA. A number of strategies can be used to design the binding specificity of the zinc finger binding domain. One approach, termed “modular assembly”, relies on the functional autonomy of individual zinc fingers with DNA. In this approach, a given sequence is targeted by identifying zinc fingers for each component triplet in the sequence and linking them into a 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 finger protein. Engineering methods include, for example, rational design and various types of selection. Rational design includes, for example, the use of databases of triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, e.g., US Patents 6,453,242 and 6,534,261, both incorporated herein by reference in their entirety. Exemplary selection methods (e.g., phage display and yeast two-hybridsystems) 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.

[0128] In certain embodiments, the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB- 1, KHZ1, PP2C, RPF1, and / or TCP5 gene and plant cells, parts including seeds, and plants comprising the mutated CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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 for the design of DNA binding domains of any desired specificity. TALEs can be linked to a nonspecific 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 inmethods described herein (Wu et al.; Biochem Biophys Res Commun. (2014);446(l):261-6; Luo et al; Scientific Reports 6, Article number: 20657 (2016)).

[0129] 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 moleculecontaining composition. In certain embodiments, the composition is delivered using negative or positive pressure, for example, using vacuum infiltration or application of hydrodynamic or fluid pressure. In certain embodiments, the composition is introduced into a plant cell or plant protoplast, e.g., by microinjection or by disruption or deformation of the cell wall or cell membrane, for example by physical treatments such as by application of negative or positive pressure, shear forces, or treatment with a chemical or physical delivery agent such as surfactants, liposomes, or nanoparticles; see, e.g., delivery of materials to cells employing microfluidic flow through a cell-deforming constriction as described in US Published Patent Application 2014 / 0287509, incorporated by reference in its entirety herein. Other techniques useful for delivering the composition to a eukaryotic cell, plant cell or plant protoplast include: ultrasound or sonication; vibration, friction, shear stress, vortexing, cavitation; centrifugation or application of mechanical force; mechanical cell wall or cell membrane deformation or breakage; enzymatic cell wall or cell membrane breakage or permeabilization; abrasion or mechanical scarification (e.g., abrasion with carborundum or other particulate abrasive or scarification with a file or sandpaper) or chemical scarification (c.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., RNAdependent DNA endonuclease, RNA dependent DNA binding protein, RNA dependent nickase, ABE, or CBE, and / or guide RNA); see, e.g., Broothaerts etal. (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.

[0130] 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 CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, 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 CRN gene of SEQ ID NO: 1, 2, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, 12, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 16, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 26, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 36, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 46, 51, 55, 56, 60, 61, 65, 66, 70, 71, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 76, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 86, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 99, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 116, 121, or an allelic variant thereof.

[0131] 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are first prescreened by screening for phenotypic characteristics plants having at least one mutation in a CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene. 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene, or an allelic variant thereof; and / or at least one mutation in a CRN, AML4, AOC4, CYP76C-1, CYP76C-2,HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are first pre-screened by screening of phenotypic characteristics plants having at least one mutation in a CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, or an allelic variant thereof; A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof. In certain embodiments, such phenotypic characteristics include increased 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 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 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 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: CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof; PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; and soybean plants comprising at least one mutation in the endogenous soybean CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof; AML4 gene of SEQ ID NO: 11, or an allelic variant thereof; AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof; CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof; HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof; KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variantthereof; PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof; RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene and soybean plants comprising at least one mutation in the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are identified and / or selected.

[0132] 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 CRN gene (e.g., SEQ ID NO: 1, 7, or an allelic variant thereof), AML4 gene (e.g., SEQ ID NO: 11 or an allelic variant thereof), AOC4 gene (e.g., SEQ ID NO: 15, 21, or an allelic variant thereof), CYP76C-1 gene (e.g., SEQ ID NO: 25, 31, or an allelic variant thereof), CYP76C-2 gene (e.g., SEQ ID NO: 35, 41, or an allelic variant thereof), HB-1 gene (e.g., SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof), KHZ1 gene (e.g., SEQ ID NO: 75, 81, or an allelic variant thereof), PP2C gene (e.g., SEQ ID NO: 85, 91, 95, or an allelic variant thereof), RPF1 gene (e.g., SEQ ID NO: 98, 104, 111, or an allelic variant thereof), and / or TCP5 gene (e.g., SEQ ID NO: 115, 121, or an allelic variant thereof), have been subjected to one or more mutagenesis treatments. Mutations of the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 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), sodium azide, methylnitrosourea (MNU), and diepoxybutane (DEB). Suitable radiation includes x-rays, fast neutron radiation, and gamma radiation.

[0133] Soybean plant cells, parts, or plants comprising at least one mutation in the endogenous CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene 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 originallyundesired 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 CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP 5 gene.

[0134] In certain embodiments, the screening comprises analyzing pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area in one or more candidate plants or one or more candidate plant populations. In these embodiments, an increase in pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area in comparison to a wild-type or control soybean plant lacking the at least one mutation is indicative of a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation. In 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.

[0135] Methods for determining whether a soybean plant cell, plant part, or plant comprises at least one mutation in the endogenous soybean CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene are provided. Methods for determining the presence or absence of the at least one mutation can be used in, for example, breeding programs for identification, selection, introgression, and the like.

[0136] In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of a CRN gene (e.g., of SEQ ID NO: 1, 2, 7, 9, 10, or an allelic variant thereof), AML4 gene (e.g., of SEQ ID NO: 11, 12, or an allelic variant thereof), AOC4 gene (e.g., of SEQ ID NO: 15, 16, 21, 23, 24, or an allelic variant thereof), CYP76C-1 gene (e.g., SEQ ID NO: 25, 26, 31, 33, 34, or an allelic variant thereof), CYP76C-2 gene (e.g., SEQ ID NO: 35, 36, 41, 43, 44, or an allelic variant thereof), HB-1 gene (e.g., SEQ ID NO: 45, 46, 51, 53, 54, 55, 56, 58, 59, 60, 61, 63, 64, 65, 66, 68, 69, 70, 71, 73, 74, or an allelic variant thereof), KHZ1 gene (e.g., SEQ ID NO: 75, 76, 81, 83, 84, or an allelic variant thereof), PP2C gene (e.g., SEQ ID NO: 85, 86, 91, 93, 94, 95, 96, 97, or an allelic variant thereof), RPF1 gene (e.g., SEQ ID NO: 98, 99, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114) or an allelic variant thereof), and / or TCP5 gene (e.g., of SEQ ID NO: 115, 116, 121, 123, 124, 125, or an allelic variant thereof), or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 2, 7, 9, 10, 11, 12, 15, 16, 21, 23, 24, 25, 26, 31, 33, 34, 35, 36, 41, 43, 44, 45, 46, 51, 55, 56, 58, 59, 60, 61, 63, 64, 65, 66, 68, 69, 70, 71, 73, 74, 75, 76, 81, 83, 84, 85, 86, 91, 93, 94, 95, 96, 97, 98, 99, 104, 106, 107, 108, 109, 110, 111, 112, 113,114, 115, 116, 121, 123, 124, 125, 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 CRN gene (e.g., SEQ ID NO: 1, 7, or an allelic variant thereof), AML4 gene (e.g., SEQ ID NO: 11 or an allelic variant thereof), A0C4 gene (e.g., SEQ ID NO: 15, 21, or an allelic variant thereof), CYP76C-1 gene (e.g., SEQ ID NO: 25, 31, or an allelic variant thereof), CYP76C-2 gene (e.g., SEQ ID NO: 35, 41, or an allelic variant thereof), HB-1 gene (e.g., SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof), KHZ1 gene (e.g., SEQ ID NO: 75, 81, or an allelic variant thereof), PP2C gene (e.g., SEQ ID NO: 85, 91, 95, or an allelic variant thereof), RPF1 gene (e.g., SEQ ID NO: 98, 104, 111, or an allelic variant thereof), and / or TCP5 gene (e.g., SEQ ID NO: 115, 121, 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, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121 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, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121 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, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121 or an allelic variant thereof) can comprise detectable labels (e.g., fluorescent, radioactive, epitope, and chemiluminescent labels). In certain embodiments, the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene can be directly sequenced using nucleic acid sequencing technologies, including whole genome sequencing.

[0137] In certain embodiments, the methods comprise analyzing a CRN polypeptide encoded by SEQ ID NO: 1, 2, or a portion thereof, or an allelic variant thereof; an AML4 polypeptide encoded by SEQ ID NO: 11, 12, or a portion thereof, or an allelic variant thereof; an AOC4 polypeptide encoded by SEQ ID NO: 15, 16, or a portion thereof, or an allelic variant thereof; CYP76C-1 polypeptide encoded by SEQ ID NO: 25, 26, or a portion thereof, or an allelicvariant thereof; CYP76C-2 polypeptide encoded by SEQ ID NO: 35, 36, or a portion thereof, or an allelic variant thereof; HB-1 polypeptide encoded by SEQ ID NO: 45, 46, 55, 56, 60, 61, 65, 66, 70, 71, or a portion thereof, or an allelic variant thereof; KHZ1 polypeptide encoded by SEQ ID NO: 75, 76, or a portion thereof, or an allelic variant thereof; PP2C polypeptide encoded by SEQ ID NO: 85, 86, or a portion thereof, or an allelic variant thereof; RPF1 polypeptide encoded by SEQ ID NO: 98, 99, or a portion thereof, or an allelic variant thereof; and / or a TCP5 polypeptide encoded by SEQ ID NO: 115, 116, or 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.

[0138] 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.

[0139] The following numbered embodiments also form part of the present disclosure:1. A soybean plant cell comprising at least one mutation in an:(a) endogenous CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) endogenous AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) endogenous AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) endogenous CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) endogenous CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) endogenous HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) endogenous KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) endogenous PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) endogenous RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) endogenous TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.2. The soybean plant cell of embodiment 1, wherein the plant cell is homozygous for the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.3. The soybean plant cell of embodiment 1 or 2, wherein the at least one mutation comprises a loss-of-function allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the CRN gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AML4 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AOC4 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-2 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the HB-1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the KHZ1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, wherein the loss- of-function allele reduces expression of the PP2C gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the RPF1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the TCP5 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation.4. The soybean plant cell of any one of embodiments 1 to 3, wherein the at least one mutation is a non-natural mutation.5. The soybean plant cell of any one of embodiments 1 to 4, wherein the at least one mutation comprises an amorphic allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.6. The soybean plant cell of any one of embodiments 1 to 4, wherein the at least one mutation comprises a hypomorphic allele of the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP5 gene.7. The soybean plant cell of any one of embodiments 1 to 6, wherein the at least one mutation comprises a frameshift mutation or a nonsense mutation in the coding region of the:(a) CRN gene of SEQ ID NO: 1, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof.8. The soybean plant cell of any one of embodiments 1 to 7, wherein the at least one mutation comprises an internal deletion in the coding region of the:(a) CRN gene of SEQ ID NO: 1, or an allelic variant thereof, optionally wherein the internal deletion preserves the reading frame of the encoded mutant CRN protein comprising the at least one mutation with respect to amino acid residues of the mutant CRN protein which have not been deleted;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AML4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AML4 protein which have not been deleted;(c) AOC4 gene of SEQ ID NO: 15, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AOC4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AOC4 protein which have not been deleted;(d) CYP76C-1 gene of SEQ ID NO: 25, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-1 protein which have not been deleted;(e) CYP76C-2 gene of SEQ ID NO: 35, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-2 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-2 protein which have not been deleted;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant HB-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant HB-1 protein which have not been deleted;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant KHZ1 protein comprising the at least one mutation with respect to amino acid residues of the mutant KHZ1 protein which have not been deleted;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant PP2C protein comprising the at least one mutation with respect to amino acid residues of the mutant PP2C protein which have not been deleted;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant RPF1 protein comprising the at least one mutation with respect to amino acid residues of the mutant RPF1 protein which have not been deleted; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant TCP5 protein comprising the at least one mutation with respect to amino acid residues of the mutant TCP5 protein which have not been deleted.9. The soybean plant cell of any one of embodiments 1 to 8, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, or 3141 nucleotides of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, 600,700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 4000, 5000, 5253, 6000, or 6959 nucleotides of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, or 1873 nucleotides of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; essentially of, or consists of a deletion of at least one nucleotide of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2216 nucleotides of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2398 nucleotides of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10070 nucleotides of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500,3750, 4000, 4250, 4500, or 4769 nucleotides of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000, 5250, 5500, 5750, or 6059 nucleotides of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, or 3939 nucleotides of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, or 4718 nucleotides of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.10. The soybean plant cell of any one of embodiments 1 to 8, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 914 nucleotides corresponding to nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation comprises, consists essentially of, orconsists 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, or 471 nucleotides corresponding to nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 402 nucleotides corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 903 nucleotides corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, or 2082 nucleotides corresponding to nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 ofthe HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 846 nucleotides corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971,5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 763 nucleotides corresponding to nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 182 nucleotides corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides corresponding to nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, or 1164 nucleotides corresponding to nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.11. The soybean plant cell of any one of embodiments 1 to 8, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof(c) nucleotides 337-361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 337- 361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 230-254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 415-439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 415- 439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.12. The soybean plant cell of any one of embodiments 1 to 11, with the proviso that the soybean plant cell is not exclusively produced by an essentially biological method, optionally wherein the soybean plant cell is produced by introducing one or more gene editing molecules into a soybean plant cell and selecting the soybean plant cell comprising at least one non-natural mutation.13. The soybean plant cell of any one of embodiments 1 to 12, wherein the soybean plant cell comprises elite soybean germplasm, optionally wherein the elite soybean germplasm comprises germplasm of a soybean cultivar or variety.14. The soybean plant cell of any one of embodiments 1 to 13, wherein the soybean plant cell further comprises at least one mutation in a distinct soybean gene.15. The soybean plant cell of embodiment 14, wherein the soybean plant cell further comprises at least one mutation in the soybean AlPlOa, AlPlOb, BS1, BS2, FTla, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene.16. The soybean plant cell of any one of embodiments 1 to 15, wherein the soybean plant cell further comprises one or more transgenes, optionally wherein the transgenes encode proteins or RNAs conferring herbicide tolerance or pest tolerance.17. The soybean plant cell of embodiment 16, wherein the soybean plant cell further comprises an A2704-12, A5547-127, BPS-CV127-9, DAS44406-6, DAS68416-4, DAS81419-2, DP305423, GTS 40- 3-2, HOS, A5547-127, MON87701, MON87705, MON87708, MON87769, MON89788, MON98788, MST-FG072-3, or SYHT0H210 transgenic event or modification thereof.18. A soybean plant part comprising the soybean plant cell of any one of embodiments 1-17.19. The soybean plant part of embodiment 18, wherein the part is a stem, root, leaf, flower, pod, or seed.20. The soybean plant part of embodiment 19, wherein the part is a seed.21. A soybean seed lot comprising the seed of embodiment 20, optionally wherein the seed lot comprises elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the mutation.22. A soybean plant comprising the soybean plant cell of any one of embodiments 1-17.23. The soybean plant of embodiment 22, wherein the soybean plant comprises increased 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, and / or percentage of 4 seeded pods for a wild-type or control soybean plant lacking the at least one mutation, optionally wherein the increased seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods is on the main stem and / or branches.24. The soybean plant of embodiment 22, wherein yield is increased in comparison to yield for a wild-type or control soybean plant 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.25. A plant or plant part of an elite soybean plant, cultivar, or variety with increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield comprising at least one mutation in the endogenous:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; wherein the increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is in comparison to a wild-type or control soybean plant lacking the at least one mutation, and optionally wherein the plant part is a seed.26. The plant or plant part of embodiment 25, wherein the elite soybean plant, cultivar, or variety is homozygous for the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.27. The plant or plant part of embodiment 25 or 26, wherein the at least one mutation comprises a loss-of-function allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the CRN gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AML4 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AOC4 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the HB-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the KHZ1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, wherein the loss- of-function allele reduces expression of the PP2C gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the RPF1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the TCP5 gene relative to a wild-type or control plant or plant part lacking the at least one mutation.28. The plant or plant part of any one of embodiments 25 to 27, wherein the at least one mutation is a non-natural mutation.29. A biological sample comprising a nucleic acid containing at least one mutation in the soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.30. The biological sample of embodiment 29, wherein the sample comprises seed meal or a tissue sample homogenate, optionally wherein the tissue sample comprises a sample of leaf, flower, pod, seed, stem, or root tissue.31. The biological sample of embodiment 29 or 30, wherein the at least one mutation is a non-natural mutation.32. The biological sample of any one of embodiments 29 to 31, wherein the at least one mutation comprises a frameshift mutation or a nonsense mutation in the coding region of the:(a) CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof.33. The biological sample of any one of embodiments 29 to 31, wherein the at least one mutation comprises an internal deletion in the coding region of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the internal deletion preserves the reading frame of the encoded mutant CRN protein comprising the at least one mutation with respect to amino acid residues of the mutant CRN protein which have not been deleted;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AML4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AML4 protein which have not been deleted;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AOC4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AOC4 protein which have not been deleted;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-1 protein which have not been deleted;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-2 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-2 protein which have not been deleted;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant HB-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant HB-1 protein which have not been deleted;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant KHZ1 protein comprising the at least one mutation with respect to amino acid residues of the mutant KHZ1 protein which have not been deleted;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant PP2C protein comprising the at least one mutation with respect to amino acid residues of the mutant PP2C protein which have not been deleted;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant RPF1 protein comprising the at least one mutation with respect to amino acid residues of the mutant RPF1 protein which have not been deleted; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant TCP5 protein comprising the at least one mutation with respect to amino acid residues of the mutant TCP5 protein which have not been deleted.34. The biological sample of any one of embodiments 29 to 33, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 914 nucleotides corresponding to nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 471 nucleotides corresponding to nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 402 nucleotides corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 903 nucleotides corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, or 2082 nucleotides corresponding to nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof(f) nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 ofthe HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 846 nucleotides corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof(g) nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 763 nucleotides corresponding to nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 182 nucleotides corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides corresponding to nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, or 1164 nucleotides corresponding to nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.35. The biological sample of any one of embodiments 29 to 34, wherein the at least one mutation comprises, cons...

Claims

What is claimed is:

1. A soybean plant cell comprising at least one mutation in an:(a) endogenous CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) endogenous AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) endogenous A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) endogenous CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) endogenous CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) endogenous HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) endogenous KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) endogenous PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) endogenous RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) endogenous TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

2. The soybean plant cell of claim 1, wherein the plant cell is homozygous for the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

3. The soybean plant cell of claim 1, wherein the at least one mutation comprises a loss-of- function allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the CRN gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AML4 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the A0C4 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-2 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the HB-1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the KHZ1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, wherein the loss- of-function allele reduces expression of the PP2C gene relative to a wild-type or control soybean plant cell lacking the at least one mutation;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the RPF1 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the TCP5 gene relative to a wild-type or control soybean plant cell lacking the at least one mutation.

4. The soybean plant cell of claim 1, wherein the at least one mutation is a non-natural mutation.

5. The soybean plant cell of claim 1, wherein the at least one mutation comprises an amorphic allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

6. The soybean plant cell of claim 1, wherein the at least one mutation comprises a hypomorphic allele of the CRN, AML4, AOC4, CYP76C-1, CYP76C-2, HB-1, KHZ1, PP2C, RPF1, and / or TCP 5 gene.

7. The soybean plant cell of claim 1, wherein the at least one mutation comprises a frameshift mutation or a nonsense mutation in the coding region of the:(a) CRN gene of SEQ ID NO: 1, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof.

8. The soybean plant cell of claim 1, wherein the at least one mutation comprises an internal deletion in the coding region of the:(a) CRN gene of SEQ ID NO: 1, or an allelic variant thereof, optionally wherein the internal deletion preserves the reading frame of the encoded mutant CRN protein comprising the at least one mutation with respect to amino acid residues of the mutant CRN protein which have not been deleted;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AML4 proteincomprising the at least one mutation with respect to amino acid residues of the mutant AML4 protein which have not been deleted;(c) A0C4 gene of SEQ ID NO: 15, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant A0C4 protein comprising the at least one mutation with respect to amino acid residues of the mutant A0C4 protein which have not been deleted;(d) CYP76C-1 gene of SEQ ID NO: 25, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-1 protein which have not been deleted;(e) CYP76C-2 gene of SEQ ID NO: 35, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-2 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-2 protein which have not been deleted;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant HB-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant HB-1 protein which have not been deleted;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant KHZ1 protein comprising the at least one mutation with respect to amino acid residues of the mutant KHZ1 protein which have not been deleted;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant PP2C protein comprising the at least one mutation with respect to amino acid residues of the mutant PP2C protein which have not been deleted;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant RPF1 protein comprising the at least one mutation with respect to amino acid residues of the mutant RPF1 protein which have not been deleted; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant TCP5 protein comprising the at least one mutation with respect to amino acid residues of the mutant TCP5 protein which have not been deleted.

9. The soybean plant cell of claim 1, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, or 3141 nucleotides of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 4000, 5000, 5253, 6000, or 6959 nucleotides of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, or 1873 nucleotides of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof; essentially of, or consists of a deletion of at least one nucleotide of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2216 nucleotides of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2398 nucleotides of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10070 nucleotides of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, or 4769 nucleotides of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000, 5250, 5500, 5750, or 6059 nucleotides of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, or 3939 nucleotides of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, optionally wherein the at least one mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, or 4718 nucleotides of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

10. The soybean plant cell of claim 1, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 914 nucleotides corresponding to nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 471 nucleotides corresponding to nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 402 nucleotides corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 903 nucleotides corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800,1900, 2000, or 2082 nucleotides corresponding to nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 ofthe HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 846 nucleotides corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 763 nucleotides corresponding to nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 182 nucleotides corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotidescorresponding to nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, or 1164 nucleotides corresponding to nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

11. The soybean plant cell of claim 1, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof(c) nucleotides 337-361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 337- 361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 230-254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 415-439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 415- 439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

12. The soybean plant cell of claim 1, with the proviso that the soybean plant cell is not exclusively produced by an essentially biological method, optionally wherein the soybean plant cell is produced by introducing one or more gene editing molecules into a soybean plant cell and selecting the soybean plant cell comprising at least one non-natural mutation.

13. The soybean plant cell of claim 1, wherein the soybean plant cell comprises elite soybean germplasm, optionally wherein the elite soybean germplasm comprises germplasm of a soybean cultivar or variety.

14. The soybean plant cell of claim 1, wherein the soybean plant cell further comprises at least one mutation in a distinct soybean gene.

15. The soybean plant cell of claim 14, wherein the soybean plant cell further comprises at least one mutation in the soybean AlPlOa, AlPlOb, BS1, BS2, FT la, JAG1, JAG2, NF-YC4, RIC1, RIC2, and / or TFLlb gene.

16. The soybean plant cell of claim 1, wherein the soybean plant cell further comprises one or more transgenes, optionally wherein the transgenes encode proteins or RNAs conferring herbicide tolerance or pest tolerance.

17. The soybean plant cell of claim 16, wherein the soybean plant cell further comprises an A2704-12, A5547-127, BPS-CV127-9, DAS44406-6, DAS68416-4, DAS81419-2, DP305423, GTS 40- 3-2, HOS, A5547-127, MON87701, MON87705, MON87708, MON87769, MON89788, MON98788, MST-FG072-3, or SYHT0H210 transgenic event or modification thereof.

18. A soybean plant part comprising the soybean plant cell of any one of claims 1-17.

19. The soybean plant part of claim 18, wherein the part is a stem, root, leaf, flower, pod, or seed.

20. The soybean plant part of claim 19, wherein the part is a seed.

21. A soybean seed lot comprising the seed of claim 20, optionally wherein the seed lot comprises elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the mutation.

22. A soybean plant comprising the soybean plant cell of any one of claims 1-17.

23. The soybean plant of claim 22, wherein the soybean plant comprises increased 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, and / or percentage of 4 seeded pods for a wild-type or control soybean plant lacking the at least one mutation, optionally wherein the increased seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods is on the main stem and / or branches.

24. The soybean plant of claim 22, wherein yield is increased in comparison to yield for a wild-type or control soybean plant 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.

25. A plant or plant part of an elite soybean plant, cultivar, or variety with increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield comprising at least one mutation in the endogenous:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; wherein the increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is in comparison to a wild-type or control soybean plant lacking the at least one mutation, and optionally wherein the plant part is a seed.

26. The plant or plant part of claim 25, wherein the elite soybean plant, cultivar, or variety is homozygous for the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

27. The plant or plant part of claim 25, wherein the at least one mutation comprises a loss-of- function allele of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the CRN gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AML4 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the AOC4 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the CYP76C-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the HB-1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the KHZ1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, wherein the loss- of-function allele reduces expression of the PP2C gene relative to a wild-type or control plant or plant part lacking the at least one mutation;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, wherein the loss-of-function allele reduces expression of the RPF1 gene relative to a wild-type or control plant or plant part lacking the at least one mutation; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, wherein the loss-of- function allele reduces expression of the TCP5 gene relative to a wild-type or control plant or plant part lacking the at least one mutation.

28. The plant or plant part of claim 25, wherein the at least one mutation is a non-natural mutation.

29. A biological sample comprising a nucleic acid containing at least one mutation in the soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

30. The biological sample of claim 29, wherein the sample comprises seed meal or a tissue sample homogenate, optionally wherein the tissue sample comprises a sample of leaf, flower, pod, seed, stem, or root tissue.

31. The biological sample of claim 29, wherein the at least one mutation is a non-natural mutation.

32. The biological sample of claim 29, wherein the at least one mutation comprises a frameshift mutation or a nonsense mutation in the coding region of the:(a) CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, or an allelic variant thereof.

33. The biological sample of claim 29, wherein the at least one mutation comprises an internal deletion in the coding region of the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the internal deletion preserves the reading frame of the encoded mutant CRN protein comprising the at least one mutation with respect to amino acid residues of the mutant CRN protein which have not been deleted;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AML4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AML4 protein which have not been deleted;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant AOC4 protein comprising the at least one mutation with respect to amino acid residues of the mutant AOC4 protein which have not been deleted;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-1 protein which have not been deleted;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant CYP76C-2 protein comprising the at least one mutation with respect to amino acid residues of the mutant CYP76C-2 protein which have not been deleted;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant HB-1 protein comprising the at least one mutation with respect to amino acid residues of the mutant HB-1 protein which have not been deleted;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant KHZ1 protein comprising the at least one mutation with respect to amino acid residues of the mutant KHZ1 protein which have not been deleted;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant PP2C protein comprising the at least one mutation with respect to amino acid residues of the mutant PP2C protein which have not been deleted;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant RPF1 protein comprising the at least one mutation with respect to amino acid residues of the mutant RPF1 protein which have not been deleted; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof optionally wherein the internal deletion preserves the reading frame of the encoded mutant TCP5 protein comprising the at least one mutation with respect to amino acid residues of the mutant TCP5 protein which have not been deleted.

34. The biological sample of claim 29, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 914 nucleotides corresponding to nucleotides 988-1901 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 471 nucleotides corresponding to nucleotides 2458 to 2925 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 402 nucleotides corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 903 nucleotides corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, or 2082 nucleotides corresponding to nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof(f) nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 ofthe HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 846 nucleotides corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof(g) nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 763 nucleotides corresponding to nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 182 nucleotides corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides corresponding to nucleotides 120-1955 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, 950, 1000, 1050, 1100, or 1164 nucleotides corresponding to nucleotides 1412-2575 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

35. The biological sample of claim 29, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 337-361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 337- 361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 230-254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation comprises, consistsessentially 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, or 25 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 415-439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 415- 439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

36. The biological sample of claim 29, wherein the sample lacks a nucleic acid comprising the wild-type allele of the soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

37. A polynucleotide comprising at least one mutation relative to the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, optionally wherein the polynucleotide is isolated;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, optionally wherein the polynucleotide is isolated; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, optionally wherein the polynucleotide is isolated.

38. The polynucleotide of claim 37, wherein the at least one mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 337-361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 337- 361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof(g) nucleotides 230-254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of the KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 415-439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 415- 439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof.

39. A method of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising the soybean plant of claim 22; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot.

40. The method of claim 39, wherein the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, 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.

41. A method of producing a soybean crop comprising planting the seed lot of claim 21.

42. The method of claim 41, further comprising harvesting seed from soybean crop grown from the planted seed.

43. The method of claim 41, wherein the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of a wild-type or control soybean crop lacking the at least one mutation, optionally wherein yield comprises pod countper plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.

44. A method for producing a soybean by-product comprising at least one processing step of cleaning, cracking, flaking, crushing, macerating, pressing, extracting, expelling, and / or extruding the seed lot of claim 21.

45. The method of claim 44, wherein the by-product is soybean protein and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; (ii) extracting the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) with an organic solvent to produce defatted soymeal; and (iii) extracting the defatted soymeal from step (ii) with an aqueous solvent to produce an aqueous fraction comprising soybean protein.

46. The method of claim 44, wherein the by-product is soybean oil and wherein the soybean seed lot is pressed to produce the oil.

47. The method of claim 44, wherein the by-product is soybean oil and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; and (ii) solvent extracting, expelling, and / or extruding step the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) to produce the oil.

48. A guide RNA molecule comprising a spacer RNA molecule which targets the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 4, 5, or 6;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 14;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 18, 19, or 20;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 28, 29, or 30;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 38, 39, or 40;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 48, 49, or 50;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 78, 79, or 80;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 88, 89, or 90;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 101, 102, or 103; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 118, 119, or 120.

49. A guide RNA molecule comprising a Casl2 direct repeat element which is fused to the spacer RNA of claim 48.

50. A gene editing system comprising: a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

51. An expression cassette comprising: a polynucleotide encoding CRISPR-Cas effector protein comprising a cleavage domain and the guide RNA molecule of claim 48.

52. A method for generating a soybean plant cell of claim 1, soybean plant part of claim 18, or soybean plant of claim 22 comprising introducing at least one mutation in the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; of a soybean plant cell.

53. The method of claim 52, further comprising regenerating a soybean plant comprising the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; from the soybean plant cell, and optionally selecting a soybean plant with increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield, optionally wherein increased yield comprises increased pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.

54. The method of claim 52, wherein the at least one mutation is introduced by:(i) directing both:(A) a guide RNA (gRNA) molecule comprising a spacer RNA molecule which targets the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 4, 5, or 6;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 14;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 18, 19, or 20;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 28, 29, or 30;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 38, 39, or 40;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 48, 49, or 50;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 78, 79, or 80;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 88, 89, or 90;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 101, 102, or 103; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 118, 119, or 120; and(B) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule to the genome of a target soybean plant cell; and(ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

55. The method of claim 54, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell.

56. The method of claim 54, wherein the soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation is identified by:(i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelic variant thereof encoded by a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelic variant thereof in one or more candidate plant cells, plant parts, or plants;(ii) analyzing a polypeptide encoded by a portion of SEQ ID NO: 1, 11, 15, 25, 35, 45, 55, 60, 65, 70, 75, 85, 95, 98, 111, and / or 115 in one or more candidate plant cells, plant parts, or plants; and / or(iii) analyzing seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield in comparison to a wild-type or control soybean plant lacking the at least one mutation is indicative of a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation, 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.

57. The method of claim 52, wherein the at least one mutation is introduced by crossing a soybean plant comprising the at least one mutation with a second soybean plant and harvesting Fl seed comprising the at least one mutation, thereby producing progeny soybean seed comprising the at least one mutation.

58. A method for generating a soybean plant cell of claim 1, soybean plant part of claim 18, or soybean plant of claim 22 comprising:(i) screening a population of soybean plant cells, parts, or plants for the presence of the at least one mutation in the endogenous(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; and(ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

59. The method of claim 58, wherein the population of soybean plant cells, parts, or plants have been subjected to one or more mutagenesis treatments, optionally wherein the mutagenesis procedure comprises chemical mutagenesis.

60. The method of claim 58, wherein the screening comprises:(i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelicvariant thereof or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelic variant thereof from one or more candidate plant cells, plant parts, or plants, wherein 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; and / or(ii) analyzing a polypeptide encoded by SEQ ID NO: 1, 11, 15, 25, 35, 45, 55, 60, 65, 70, 75, 85, 95, 98, 111, and / or 115, a portion thereof, or an allelic variant thereof from one or more candidate plant cells, plant parts, or plants, wherein 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.

61. The method of claim 58, wherein the screening further comprising analyzing seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield in comparison to a wild-type or control soybean plant lacking the at least one mutation, wherein increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is indicative of a soybean plant cell, soybean plant part, or soybean plant comprising 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.

62. A method for increasing seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield in a soybean plant, comprising: introducing at least one mutation in the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; of a soybean plant cell.

63. The method of claim 62, further comprising regenerating a soybean plant comprising the at least one mutation in the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; from the soybean plant cell, and optionally selecting a soybean plant with increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield.

64. The method of claim 62, wherein the at least one mutation is introduced by:(i) directing both:(A) a guide RNA (gRNA) molecule comprising a spacer RNA molecule which targets the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 4, 5, or 6;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 14;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 18, 19, or 20;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 28, 29, or 30;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 38, 39, or 40;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 48, 49, or 50;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 78, 79, or 80;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 88, 89, or 90;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 101, 102, or 103; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof, or a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 118, 119, or 120; and(B) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule to the genome of a target soybean plant cell; and(ii) isolating a soybean plant cell or soybean plant comprising the at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

65. The method of claim 64, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell.

66. The method of claim 62, wherein the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of a wild-type or control soybean crop 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.

67. A soybean plant or plant cell produced by the method of claim 62.

68. A method for determining whether a soybean plant cell, plant part, or plant comprises at least one mutation of the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) A0C4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; the method comprising:(i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 75, 81, 85, 91, 98, 104, 115, and / or 121, or an allelic variant thereof or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelic variant thereof from the plant cell, plant part, or plant, wherein an insertion, deletion, and / or substitution of one or more nucleotides in the polynucleotide or RNA is indicative of the presence of the at least one mutation; and / or(ii) analyzing a polypeptide encoded by SEQ ID NO: 1, 11, 15, 25, 35, 45, 55, 60, 65, 70, 75, 85, 95, 98, 111, and / or 115, a portion thereof, or an allelic variant thereof from the soybean plant cell, plant part, or plant, wherein an insertion, deletion, and / or substitution of one or more amino 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.

69. The method of claim 68, wherein the method further comprises analyzing seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield in comparison to a wildtype or control soybean plant lacking the at least one mutation, wherein increased seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield is indicative of a soybean plant cell, soybean plant part, or soybean plant comprising 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.

70. A method for determining whether a soybean seed lot comprises soybean seed comprising at least one mutation of the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; the method comprising:(i) analyzing a polynucleotide comprising a portion of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121, or an allelic variant thereof or analyzing an RNA encoded by a portion of SEQ ID NO: 1, 11, 15, 25, 35, 45, 55, 60, 65, 70, 75, 85, 95, 98, 111, and / or 115, or an allelic variant thereof from a sample of the soybean seed lot, wherein 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; and / or(ii) analyzing a polypeptide encoded by SEQ ID NO: 1, 11, 15, 25, 35, 45, 55, 60, 65, 70, 75, 85, 95, 98, 111, and / or 115, a portion thereof, or an allelic variant thereof from a sample of the soybean seed lot, wherein 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.

71. Use of the soybean plant cell of claim 1, the soybean plant part of claim 18, the soybean seed lot of claim 21, or the soybean plant of claim 22 to produce soybean seed.

72. Use of the soybean plant cell of claim 1, the soybean plant part of claim 18, the soybean seed lot of claim 21, or the soybean plant of claim 22 to grow a soybean crop.

73. Use of the soybean plant cell of claim 1, the soybean plant part of claim 18, the soybean seed lot of claim 21, or the soybean plant of claim 22 to obtain a soybean by-product.

74. The use of claim 73, wherein the soybean by-product comprises soybean flour, meal, protein, oil, syrup, or starch.

75. Use of the guide RNA molecule of claim 48, the gene editing system of claim 50, or the expression cassette of claim 51 to introduce at least one mutation in the endogenous soybean:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11 or an allelic variant thereof; and / or(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

76. A soybean plant cell, soybean plant part, or soybean plant obtainable by the process comprising:(i) directing both:(A) a guide RNA (gRNA) molecule comprising a spacer RNA molecule which targets the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21, or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof; and(B) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule to the genome of a target soybean plant cell; and(ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at least one mutation in the:(a) CRN gene of SEQ ID NO: 1, 7, or an allelic variant thereof;(b) AML4 gene of SEQ ID NO: 11, or an allelic variant thereof;(c) AOC4 gene of SEQ ID NO: 15, 21 or an allelic variant thereof;(d) CYP76C-1 gene of SEQ ID NO: 25, 31, or an allelic variant thereof;(e) CYP76C-2 gene of SEQ ID NO: 35, 41, or an allelic variant thereof;(f) HB-1 gene of SEQ ID NO: 45, 51, 55, 60, 65, 70, or an allelic variant thereof;(g) KHZ1 gene of SEQ ID NO: 75, 81, or an allelic variant thereof;(h) PP2C gene of SEQ ID NO: 85, 91, 95, or an allelic variant thereof;(i) RPF1 gene of SEQ ID NO: 98, 104, 111, or an allelic variant thereof; and / or(j) TCP5 gene of SEQ ID NO: 115, 121, or an allelic variant thereof.

77. The soybean plant cell, soybean plant part, or soybean plant of claim 76, wherein the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: SEQ ID NO: 4, 5, 6, 14, 18, 19, 20, 28, 29, 30, 38, 39, 40, 48, 49, 50, 78, 79, 80, 88, 89, 90, 101, 102, 103, 118, 119, or 120.

78. The soybean plant cell, soybean plant part, or soybean plant of claim 76, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell.

79. The soybean plant cell, soybean plant part, or soybean plant of claim 76, wherein the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield isincreased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of a wild-type or control soybean crop 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.

80. A soybean genome characterized by the fact that it comprises a non-natural mutation in the nucleotide sequence of SEQ ID NO: 1, 7, 11, 15, 21, 25, 31, 35, 41, 45, 51, 55, 60, 65, 70, 75, 81, 85, 91, 95, 98, 104, 111, 115, and / or 121.

81. The soybean genome of claim 80, wherein the non-natural mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide of:(a) SEQ ID NO: 1 or 7, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, or 3141 nucleotides of SEQ ID NO: 1;(b) SEQ ID NO: 11, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 4000, 5000, 5253, 6000, or 6959 nucleotides of SEQ ID NO: 11;(c) SEQ ID NO: 15 or 21, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, or 1873 nucleotides of SEQ ID NO: 15;(d) SEQ ID NO: 25 or 31, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2216 nucleotides of SEQ ID NO: 25;(e) SEQ ID NO: 35 or 41, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, or 2398 nucleotides of SEQ ID NO: 35;(f) SEQ ID NO: 45, 51, 55, 60, 65, or 70, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, or 10070 nucleotides of SEQ ID NO: 45;(g) SEQ ID NO: 75 or 81, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, or 4769 nucleotides of SEQ ID NO: 75;(h) SEQ ID NO: 85, 91, or 95, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4250, 4500, 4750, 5000, 5250, 5500, 5750, or 6059 nucleotides of SEQ ID NO: 85;(i) SEQ ID NO: 98, 104, or 111, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, or 3939 nucleotides of SEQ ID NO: 98; and / or(j) SEQ ID NO: 115 or 121, optionally wherein the non-natural mutation 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, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, or 4718 nucleotides of SEQ ID NO: 115.

82. The soybean genome of claim 80, wherein the non-natural mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 988-1901 of the CRN gene (SEQ ID NO: 1), optionally wherein the nonnatural mutation 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, or 914 nucleotides corresponding to nucleotides 988- 1901 of SEQ ID NO: 1, or an allelic variant thereof;(b) nucleotides 2458 to 2925 of the AML4 gene (SEQ ID NO: 11), optionally wherein the non-natural mutation 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, or 471 nucleotides corresponding to nucleotides 2458 to 2925 of SEQ ID NO: 11, or an allelic variant thereof;(c) nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene (SEQ ID NO: 15) or an allelic variant thereof, optionally wherein the at least one mutation 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, or 402 nucleotides corresponding to nucleotides 342-591, 695-816, and 1254-1655 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene (SEQ ID NO: 25) or an allelic variant thereof, optionally wherein the at least one mutation 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, or 903 nucleotides corresponding to nucleotides 142-1044 and 1199-1828 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 60-971 and 1471-2082 of the CYP76C-2 gene (SEQ ID NO: 35), optionally wherein the non-natural mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, or2082 nucleotides corresponding to nucleotides 60-971 and 1471-2082 of SEQ ID NO: 35 or an allelic variant thereof;(f) nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 ofthe HB-1 gene (SEQ ID NO: 45), optionally wherein the non-natural mutation 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, or 846 nucleotides corresponding to nucleotides 790-985, 1159-1593, 1952-2034, 2708-3118, 3228-3308, 3414-3578, 3674-3896, 4033-4133, 4635-4721, 4819-4971, 5056-5211, 5599-5808, 5887-6546, 6631-7182, 7336-7956, 8068-8172, 8280-8543, and 8836-9681 of SEQ ID NO: 45 or an allelic variant thereof;(g) nucleotides 205-274, 684-744, and 3855-4617 of the KHZ1 gene (SEQ ID NO: 75), optionally wherein the non-natural mutation 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, or 763 nucleotides corresponding to nucleotides 205-274, 684-744, and 3855-4617 of SEQ ID NO: 75 or an allelic variant thereof;(h) nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303-4374, and 5216-5344 of the PP2C gene (SEQ ID NO: 85), optionally wherein the non-natural mutation 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, or 182 nucleotides corresponding to nucleotides 73-254, 2058-2200, 3043-3141, 3272-3430, 3717-3803, 4108-4199, 4303- 4374, and 5216-5344 of SEQ ID NO: 85 or an allelic variant thereof;(i) nucleotides 120-1955 of the RPF1 gene (SEQ ID NO: 98), optionally wherein the non-natural mutation 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, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, or 1836 nucleotides corresponding to nucleotides 120-1955 of SEQ ID NO: 98 or an allelic variant thereof; and / or(j) nucleotides 1412-2575 of the TCP5 gene (SEQ ID NO: 115), optionally wherein the non-natural mutation 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, 950, 1000, 1050, 1100, or 1164 nucleotides corresponding to nucleotides 1412-2575 of SEQ ID NO: 115.

83. The soybean genome of claim 80, wherein the non-natural mutation comprises, consists essentially of, or consists of a deletion of at least one nucleotide corresponding to:(a) nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 1225-1249, 1248-1272, or 1811-1835 of the CRN gene of SEQ ID NO: 1 or an allelic variant thereof;(b) nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 2614 to 2638 of the AML4 gene of SEQ ID NO: 11 or an allelic variant thereof;(c) nucleotides 337-361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 337- 361, 382-406, or 418-442 of the AOC4 gene of SEQ ID NO: 15 or an allelic variant thereof;(d) nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof, optionally wherein the at least one mutation 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, or 25 nucleotides corresponding to nucleotides 294-318, 453-477, or 557-581 of the CYP76C-1 gene of SEQ ID NO: 25 or an allelic variant thereof;(e) nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 149-173, 239-263, or 292-316 of the CYP76C-2 gene of SEQ ID NO: 35(f) nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 2720-2744, 2809-2833, or 2955-2979 of the HB-1 gene of SEQ ID NO: 45;(g) nucleotides 230-254, 715-739, or 3943-3967 of KHZ1 gene of SEQ ID NO: 75 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 230- 254, 715-739, or 3943-3967 of KHZ1 gene of SEQ ID NO: 75;(h) nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 3097-3121, 3296-3320, or 3734-3758 of the PP2C gene of SEQ ID NO: 85;(i) nucleotides 415-439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 415- 439, 675-699, or 770-794 of the RPF1 gene of SEQ ID NO: 98; and / or(j) nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115 or an allelic variant thereof, optionally wherein the non-natural mutation 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, or 25 nucleotides corresponding to nucleotides 1535-1559, 1638-1662, or 1779-1803 of the TCP5 gene of SEQ ID NO: 115.

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