Methods and compositions for improving seed from oilseed plants

Abstract

Methods and compositions for improving seed (e.g., increasing seed size, increasing seed yield) are described herein.

Description

[0001] F&R Ref No.: 09531-0556WO1 METHODS AND COMPOSITIONS FOR IMPROVING SEED FROM OILSEED PLANTS FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was made with government support under IOS1933291 awarded by National Science Foundation. The government has certain rights in the invention. TECHNICAL FIELD This disclosure generally relates to methods and compositions for engineering plants to improve seed. BACKGROUND Improving seed size has always been a priority for the breeders, however, traditional breeding has had limited success in effectively improving seed size. The methods described herein provide multiple paths to increasing seed size. SUMMARY Described herein are methods and compositions for improving seed (e.g., increasing seed size, increasing seed yield) In one aspect, modified oilseed plants exhibiting increased seed size and seed yield relative to a corresponding non-modified oilseed plant are provided. Such modified oilseed plants have an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide. In some embodiments, the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:113. In some embodiments, the modified oilseed plant comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111. In some embodiments, the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:111. In some embodiments, the modified oilseed plant further comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ F&R Ref No.: 09531-0556WO1 ID NO:112. In some embodiments, the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:112. In some embodiments, the modified oilseed plant further comprises an endogenous nucleic acid encoding an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:114, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL15 polypeptide. In some embodiments, the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:114. In some embodiments, the oil seed plant is selected from Camelina, pennycress, canola or soybean. In another aspect, methods of increasing seed size and seed yield in an oil seed plant are provided. Such methods typically include disrupting expression of a first endogenous nucleic acid molecule in cells from the oil seed plant, wherein, prior to disrupting, the first endogenous nucleic acid molecule encodes an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the oil seed plant expresses little to no AGL9 polypeptide. In some embodiments, expression of the first endogenous nucleic acid molecule in the cells from the oil seed plant is disrupted using gene editing. In some embodiments, the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:113. In some embodiments, introducing a first exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the first exogenous nucleic acid molecule encodes an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111. In some embodiments, the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:111. In some embodiments, the methods further include introducing a second exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the second exogenous nucleic acid molecule encodes an SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112. In some embodiments, the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:112. In some embodiments, such methods further include: disrupting expression of a second endogenous nucleic acid molecule in the cells from the oil seed plant, wherein, prior to disrupting, the second endogenous nucleic acid molecule encodes an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:114. In some F&R Ref No.: 09531-0556WO1 embodiments, the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:114. In some embodiments, the oil seed plant is selected from Camelina, pennycress, canola or soybean. In some embodiments, expression and / or activity of endogenous MINI3 and / or endogenous IKU2 is / are increased in the oil seed plant. In still another aspect, methods of increasing seed size and seed yield in an oil seed plant are provided. Such methods typically include a) providing a first modified oilseed plant, wherein the modified oilseed plant comprises an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide; b) providing a second modified oilseed plant, wherein the second modified oilseed plant: i) comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111, or ii) comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112; and c) crossing the first modified plant with the second modified plant to produce progeny plants, wherein the progeny plants exhibit increased seed size and seed yield. In some embodiments, the first and the second oilseed plants are selected from Camelina, pennycress, canola or soybean. In one aspect, methods of promoting endosperm proliferation to increase seed size and seed yield in an oil seed plant are provided. Such methods typically include engineering the plant genome to increase the expression of ARR11. In some embodiments, the methods further include engineering the plant genome to increase the expression of SHB1. In some embodiments, the methods further include engineering the plant genome to disrupt and / or knock out AGL9. In some embodiments, the methods further include engineering the plant genome to disrupt and / or knock out AGL15. In some embodiments, engineering the plant genome to increase the expression of ARR11 comprises overexpressing an exogenous nucleic acid encoding ARR11. In some embodiments, engineering the plant genome to increase the expression of SHB1 includes overexpressing an exogenous nucleic acid encoding SHB1. In some embodiments, engineering the plant genome to disrupt and / or knock out AGL9 includes using CRISPR F&R Ref No.: 09531-0556WO1 technology. In some embodiments, engineering the plant genome to disrupt and / or knock out AGL15 includes using CRISPR technology. In some embodiments, the oil seed plant is Camelina, pennycress, canola or soybean. In some embodiments, expression and / or activity of MINI3 and / or IKU2 are increased. In another aspect, methods of prolonging endosperm proliferation to increase seed size and seed yield in an oil seed plant are provided. Such methods typically include engineering the plant genome to disrupt and / or knock out AGL9; and engineering the plant genome to disrupt and / or knock out AGL15. In some embodiments, the oil seed plant is Camelina, pennycress, canola or soybean. In some embodiments, expression and / or activity of MINI3 and / or IKU2 are de- repressed and / or sustained. In still another aspect, engineered oilseed plants are provided that exhibit increased seed size and seed yield relative to corresponding non-engineered oilseed plants, wherein the genome of the engineered oilseed plant is engineered to overexpress ARR11. In some embodiments, the genome of the engineered oilseed plant is further engineered to overexpress SHB1. In some embodiments, the genome of the engineered oilseed plant is further engineered to disrupt and / or knock out AGL9. In some embodiments, the genome of the engineered oilseed plant is further engineered to disrupt and / or knock out AGL15. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the methods and compositions of matter belong. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the methods and compositions of matter, suitable methods and materials are described below. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. F&R Ref No.: 09531-0556WO1 DESCRIPTION OF DRAWINGS FIG.1A-1C shows that overexpression of Arabidopsis ARR11:MYC and SHB1:FLAG in Camelina spring variety Suneson produces larger seeds (FIG.1A and 1B) and that gene editing of camelina AGL9s also enlarges camelina seeds (FIG.1A and 1C). FIG.2 is a graph showing transgenic Arabidopsis plants that overexpress ARR11. FIG.3 shows seed mass in Arabidopsis plants overexpressing ARR11. FIG.4 shows overexpression of ARR11 and SHB1 together produces even larger seeds. Seed mass of Ws, three ARR11 overexpression lines in Ws background, shb1-D, and three ARR11 overexpression lines in shb1-D background. FIG.5 shows AGL9 and AGL15 knockout and overexpression on mature seed mass, IKU2 and MINI3 expression, and MEA targeting. (5A) Seed mass of single agl9 or agl15 mutants. (5B) Seed mass of double agl9 agl15 mutants with AGL9 CRISPR in agl15-2 or agl15-3 background. Letters indicate significant deviations from Col-0 determined by two-tailed Student t-test (p<0.01, **). (5C) Seed mass of Ws, AGL9:FLAG and AGL15:FLAG transgenic plants. Seed mass was calculated from at least three biological replicates with one technical replicate per biological replicate. FIG.6 shows the results of hand pollination and reciprocal crosses on seed mass. Reciprocal crosses of Col-0 to the agl9 agl15 c3 mutant or vice versa on mature seed mass. Significant difference is indicated by two-tailed Student’s t-test, p<0.01 between a and b. FIG.7 shows the cellularization analysis of Ws, AGL9:FLAG and AGL15:FLAG transgenic seeds. Cellularized endosperm area quantified for Ws, AGL9:FLAG and AGL15:FLAG transgenic seeds from 3 to 6 DAP. Significant levels by two-tailed Student’s t-test: p<0.01 between Ws and AGL9:FLAG transgenic seeds and p<0.05 between Ws and AGL15:FLAG transgenic seeds at 3 and 4 DAP. FIG.8 shows that edits in AGL9 and AGL15 C-termini still produce large seeds but avoid silique development retardation and seed abortion. Seed mass in complete knockout of agl9-1 or agl9-2, AGL9 C-terminal edit in the background of complete AGL15 knockout (agl9 agl15-2 c1) or largely loss-of-function AGL15 (agl9 agl15-3 c3). Partial seed abortion was observed in complete knockout of agl9-1 and agl9-2, AGL9 partial knockout in the background of almost complete knockouts of AGL15 (agl9 agl15- 2 c1 or agl9 agl15-3 c3). The agl9 c agl15 c double mutant had both AGL9 and AGL15 edited close to their C-terminal ends. This double mutant produced large but not aborted F&R Ref No.: 09531-0556WO1 seeds. FIG.9 shows the mass of Camelina seeds in which AGL9 and AGL15 have been knocked out. DETAILED DESCRIPTION In angiosperms, double fertilization results in the formation of a diploid embryo and a triploid endosperm, and the endosperm is derived from the central cell that is diploid and contains two identical haploid genomes. The endosperm constitutes the major volume of mature seeds in monocots and some dicots. In many other dicots such as Arabidopsis, seed development includes two distinct phases, and the embryo grows to full size and replaces most of the endosperm at maturity. In the first phase, the endosperm grows and proliferates rapidly to generate a large multinucleate cell known as coenocyte. This larger embryo sac or seed cavity closes to the mature seed volume. The coenocyte is then partitioned into individual cells by a specific type of cytokinesis called cellularization and endosperm proliferation declines. Cellularization starts in the micropylar pole after the eighth mitotic cycle in the peripheral endosperm. In the second phase, the embryo grows rapidly at the expense of the endosperm. At maturity, the seed contains only a single layer of endosperm cells in Arabidopsis, and the maternal integument becomes the seed coat. The expression of IKU2 is specifically in the endosperm and reaches a peak in a few days after pollination (DAP) but is suppressed at 4 to 5 DAP. SHB1 directly activates the expression of IKU2 and MINI3. In addition, mutations in Fertilization Independent Seed (FIS) genes lead to autonomous endosperm proliferation in the absence of fertilization. In this case, the endosperm is over-proliferated and the embryo is aborted after fertilization. MADS-domain proteins are found in plants, animals, and fungi. Several MADS- box proteins are reported to positively regulate endosperm development. AGAMOUS- LIKE80 (AGL80) regulates early central cell development and subsequent endosperm cellularization. The agl61 mutant shows a similar central cell and endosperm phenotype as agl80. AGL80 interacts with AGL61 and recruits AGL61 to the nucleus. AGL80 also interacts with AGL62, and agl62 endosperm undergoes early cellularization. AGL62 is strongly expressed in the endosperm during the syncytial phase but sharply declines before cellularization. In some fis mutants, endosperm cellularization is blocked, but AGL62 expression remains high. In another previous report, AGL15 was found to interact F&R Ref No.: 09531-0556WO1 with members of the SWI-independent 3 / histone deacetylase (SIN3 / HDAC) complex, and AGL15 can repress transcription in general. Whether some MADS-box proteins also negatively regulate plant reproduction remains unknown. In this study, we demonstrated that AGL9 (MADS-box Agamous-like protein 9) and AGL15 (MADS-box Agamous-like protein 15) have a redundant function in the suppression of key gene expression for endosperm proliferation. AGL9 and AGL15 recruit FIS-PRC2 to key genomic loci, including IKU2 and MINI3, and repress their expression and endosperm proliferation at 4 to 5 DAP. AGL9 and AGL15 recognize the CArG elements in the IKU2 and MINI3 promoters and interact with MEA in vitro and in vivo. AGL9 and AGL15 are not expressed and do not accumulate to a high level during endosperm proliferation until 4 to 5 DAP. By 4 DAP, a relatively high level of AGL9 and AGL15 triggers the onset of IKU2 and MINI3 repression by FIS-PRC2. AGL9 and AGL15 are required for the targeting of MEA to the two genomic loci. agl9 or agl9 agl15 mutations promote endosperm proliferation and delay endosperm cellularization. CUT&Tag and RNA-seq identified genome-wide repressive H3K27me3 marks and targets of AGL9 and AGL15. Other CUT&RUN seq experiments with endosperm nuclei also reported the enriched H3K27me3 marks at the IKU2 locus about 2-fold (p<0.01) and a trimethylated MINI3 locus about 3.4-fold (p<0.01). AGL9 and AGL15 only form heterodimers but not homodimers in yeast two- hybrid assays, so it is intriguing to try to explain why a single agl15-2 or agl15-3 mutation did not show a seed mass phenotype (FIG.5A). It is possible that AGL9 or AGL15 is capable of binding DNA as monomers in vivo although dimers may increase the affinity and specificity of their binding. In addition, AGL15 is expressed at a lower magnitude than that of AGL9. Thus, the expression and activity of AGL9 may dictate a major function of AGL9 compared to that of AGL15. Further, another AGL protein may also be involved with a similar function as that of AGL9 and AGL15, but the identity of this AGL protein remains unknown. We observed a 25% silique abortion for either the agl9-1 or the agl9-2 single mutant, likely due to seed abortion. The two agl9 mutant alleles are true knockouts. A higher rate of silique abortion occurred in agl9 agl15-2 or agl9 agl15-3 double mutants, in which both agl9 and agl15-2 are knockout mutants and agl15-3 is a partial loss-of- function mutant. This strongly suggests that AGL9 and AGL15 have redundant functions. Mutations in MEDEA lead to autonomous endosperm development and seed lethality F&R Ref No.: 09531-0556WO1 from 3 to 5 DAP. In the agl9 agl15-3 c3 mutant, seed abortion occurred early at 2 DAP at a rate of around 50%. The reasons for this abortion remain unclear and might be different from mea-caused seed abortion. For example, it might be caused by defective male or female gametophyte development or fertilization. Since our double agl9 agl15 mutant contains at least one partial loss-of-function mutation, a true double knockout of AGL9 and AGL15 would lead to a complete seed abortion. The remaining 50 to 60% of seeds in various agl9 agl15 double mutants were not aborted and had an increased seed mass (FIG.5B). It is likely due to prolonged endosperm proliferation and delayed endosperm cellularization. This conclusion is based on the essential function of AGL9 and AGL15 in recruiting FIS-PRC2 for suppression of the key endosperm proliferation genes at 4 to 5 DAP. When AGL9 and AGL15 are mutated, even with a partial loss-of-function AGL9, MEA fails to target to the IKU2 and MINI3 loci and the expression of IKU2 and MINI3 were elevated at 4 to 5 DAP. On the other hand, the increased seed mass in the various agl9 agl15 double mutants could also be caused by fewer seeds in a silique. With the abortion of some seeds in a silique, more resources and space are available to support the growth of the remaining seeds. Based on these experiments, disrupting AGL9 in oilseed plants results in an increase in seed size, seed yield, and / or seed oil yield. As used herein, disrupting can refer to a complete knock-out (i.e., no expression of AGL9 polypeptides or expression of AGL9 polypeptides that are not functional) but disrupting also can refer to a significantly reduced expression of AGL9 (e.g., 20% or less AGL9 polypeptide or functionality relative to a corresponding non-disrupted oilseed plant). Thus, little to no AGL9 polypeptide following disruption refers to less than 20% (e.g., less than 10%, less than 5%, less than 2.5%, less than 1%) of the amount of AGL9 polypeptide or less than 20% (e.g., less than 10%, less than 5%, less than 2.5%, less than 1%) of the activity of the AGL9 polypeptide relative to a corresponding plant in which AGL9 has not been disrupted. In addition, overexpressing ARR11 (Arabidopsis Response Regulator 11) or SHB1 (Short Hypocotyl Under Blue 1) in combination with a disrupted AGL9 can further increase the seed size, seed yield, and / or seed oil yield in such oilseed plants. ARR11 is considered a type-B response regulator and acts as a transcription factor that plays a role in cytokinin signaling. ARR11 also appears to play a role in disease resistance as knocking out ARR11 resulted in fungal-susceptible plants. SHB1 is involved in F&R Ref No.: 09531-0556WO1 cytochrome signaling and ultimately promotes endosperm proliferation, increases mature seed size, regulates the expression of MINI3 and IKU2, and directly associates with their promoters. Different from most members of the SYG1 protein family in many organisms, SHB1 is localized to the nucleus. Nucleic Acids and Polypeptides As used herein, nucleic acids can include DNA and RNA, and includes nucleic acids that contain one or more nucleotide analogs or backbone modifications. A nucleic acid can be single stranded or double stranded, which usually depends upon its intended use. In addition to the nucleic acids and polypeptides disclosed herein (e.g., SEQ ID NOs: 94, 95, 96 and 101 encoding SEQ ID NOs: 111, 112, 113 and 114, respectively), the skilled artisan will further appreciate that random or targeted changes can be introduced into any of the nucleic acid molecules, thereby leading to changes in the amino acid sequence of the encoded polypeptide. For example, random or targeted changes can be introduced into nucleic acid coding sequences using mutagenesis (e.g., site-directed mutagenesis, PCR-mediated mutagenesis) or by chemically synthesizing a nucleic acid molecule having such changes. Nucleic acids or cells containing nucleic acids can be changed (e.g., mutagenized) using, for example, a chemical mutagen, ionizing radiation, or fast neutron bombardment (see, e.g., Li et al., 2001, Plant J., 27:235-42). Representative chemical mutagens include, without limitation, nitrous acid, sodium azide, acridine orange, ethidium bromide, and ethyl methane sulfonate (EMS), while representative ionizing radiation includes, without limitation, x-rays, gamma rays, fast neutron irradiation, and UV irradiation. Such changes in the DNA sequence generally are random and can lead to conservative and / or non- conservative amino acid substitutions at one or more amino acid residues. In addition, methods of making a specific or targeted changes (e.g., mutations) are known in the art and include, for example, TALEN technology (see, for example, Li et al., 2011, Nucleic Acids Res., 39(14):6315-25), zinc-finger technology (see, for example, Wright et al., 2005, The Plant J., 44:693-705), and CRISPR technology (see, for example, Mali et al., 2013, Nature Methods, 10:957-63). A “conservative amino acid substitution” is one in which one amino acid residue is replaced with a different amino acid residue having a similar side chain, and a non- F&R Ref No.: 09531-0556WO1 conservative substitution is one in which an amino acid residue is replaced with an amino acid residue that does not have a similar side chain. See, for example, Dayhoff et al. (1978, in Atlas of Protein Sequence and Structure, 5(Suppl.3):345-352), which provides frequency tables for amino acid substitutions. Non-conservative substitutions can change the charge or hydrophobicity of the encoded polypeptide. Non-conservative amino acid substitutions can also make a substantial change in the bulk of the residue side chain. Therefore, nucleic acids and polypeptides also are provided that differ from SEQ ID NOs: 94, 95, 96, and 101 and SEQ ID NOs: 111, 112, 113, and 114, respectively. Nucleic acids and polypeptides that differ in sequence from SEQ ID NOs: 94, 95, 96, and 101 and SEQ ID NOs: 111, 112, 113, and 114, can have at least 80% sequence identity (e.g., at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity) to SEQ ID NOs: 94, 95, 96, and 101 and SEQ ID NOs: 111, 112, 113, and 114, respectively. It would be understood that one or more differences in nucleic acid or polypeptide sequences relative to SEQ ID NOs: 94, 95, 96, and 101 and SEQ ID NOs: 111, 112, 113, and 114, respectively, can result in little to no change in expression or function of the respective sequence (e.g., compared to SEQ ID NOs: 94, 95, 96, and 101 and SEQ ID NOs: 111, 112, 113, and 114, respectively) or can disrupt (e.g., knock-out) the expression and / or function of the respective sequence. In calculating percent sequence identity, two sequences are aligned and the number of identical matches of nucleotides or amino acid residues between the two sequences is determined. The number of identical matches is divided by the length of the aligned region (i.e., the number of aligned nucleotides or amino acid residues) and multiplied by 100 to arrive at a percent sequence identity value. It will be appreciated that the length of the aligned region can be a portion of one or both sequences up to the full- length size of the shortest sequence. It also will be appreciated that a single sequence can align with more than one other sequence and hence, can have different percent sequence identity values over each aligned region. The alignment of two or more sequences to determine percent sequence identity can be performed using the algorithm described by Altschul et al. (1997, Nucleic Acids Res., 25:33893402) as incorporated into BLAST (Basic Local Alignment Search Tool) programs, available at ncbi.nlm.nih.gov on the World Wide Web. BLASTN is the program used to align and compare the identity between nucleic acid sequences, while BLASTP is the program used to align and compare the identity between amino acid F&R Ref No.: 09531-0556WO1 sequences. When utilizing BLAST programs to calculate the percent identity between a sequence and another sequence, the default parameters of the respective programs generally are used. As used herein, an “isolated” nucleic acid molecule is a nucleic acid molecule that is free of sequences that naturally flank one or both ends of the nucleic acid in the genome of the organism from which the isolated nucleic acid molecule is derived (e.g., a cDNA or genomic DNA fragment produced by PCR or restriction endonuclease digestion). Such an isolated nucleic acid molecule is generally introduced into a vector (e.g., a cloning vector, or an expression vector) for convenience of manipulation or to generate a fusion nucleic acid molecule, discussed in more detail below. In addition, an isolated nucleic acid molecule can include an engineered nucleic acid molecule such as a recombinant or a synthetic nucleic acid molecule. Nucleic acids can be isolated using techniques routine in the art. For example, nucleic acids can be isolated using any method including, without limitation, recombinant nucleic acid technology, and / or the polymerase chain reaction (PCR). General PCR techniques are described, for example in PCR Primer: A Laboratory Manual, Dieffenbach & Dveksler, Eds., Cold Spring Harbor Laboratory Press, 1995. Recombinant nucleic acid techniques include, for example, restriction enzyme digestion and ligation, which can be used to isolate a nucleic acid. Isolated nucleic acids also can be chemically synthesized, either as a single nucleic acid molecule or as a series of oligonucleotides. As used herein, a “purified” polypeptide is a polypeptide that has been separated or purified from cellular components that naturally accompany it. Typically, the polypeptide is considered “purified” when it is at least 70% (e.g., at least 75%, 80%, 85%, 90%, 95%, or 99%) by dry weight, free from the proteins and naturally occurring molecules with which it is naturally associated. Since a polypeptide that is chemically synthesized is, by nature, separated from the components that naturally accompany it, a synthetic polypeptide is “purified.” Polypeptides can be purified from natural sources (e.g., a biological sample) by known methods such as DEAE ion exchange, gel filtration, and hydroxyapatite chromatography. A polypeptide also can be purified, for example, by expressing a nucleic acid in an expression vector. In addition, a purified polypeptide can be obtained by chemical synthesis. The extent of purity of a polypeptide can be measured using any F&R Ref No.: 09531-0556WO1 appropriate method, e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. A construct or vector containing a nucleic acid (e.g., a nucleic acid that encodes a polypeptide) also is provided. Constructs or vectors, including expression constructs or vectors, are commercially available or can be produced by recombinant DNA techniques routine in the art. A construct or vector containing a nucleic acid can have expression elements operably linked to such a nucleic acid, and further can include sequences such as those encoding a selectable marker (e.g., an antibiotic resistance gene). A construct or vector containing a nucleic acid can encode a chimeric or fusion polypeptide (i.e., a polypeptide operatively linked to a heterologous polypeptide, which can be at either the N-terminus or C-terminus of the polypeptide). Representative heterologous polypeptides are those that can be used in purification of the encoded polypeptide (e.g., 6xHis tag, glutathione S-transferase (GST)) Expression elements include nucleic acid sequences that direct and regulate expression of nucleic acid coding sequences. One example of an expression element is a promoter sequence. Expression elements also can include introns, enhancer sequences, response elements, or inducible elements that modulate expression of a nucleic acid. Expression elements can be of bacterial, yeast, insect, mammalian, or viral origin, and vectors can contain a combination of elements from different origins. As used herein, operably linked means that a promoter or other expression element(s) are positioned in a vector relative to a nucleic acid in such a way as to direct or regulate expression of the nucleic acid. Constructs or vectors as described herein can be introduced into a host cell. As used herein, “host cell” refers to the particular cell into which the nucleic acid is introduced and also includes the progeny or potential progeny of such a cell. A host cell can be any prokaryotic or eukaryotic cell. For example, nucleic acids can be introduced into bacterial cells such as E. coli, or in insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art. Many methods for introducing nucleic acids into host cells, both in vivo and in vitro, are well known to those skilled in the art and include, without limitation, electroporation, calcium phosphate precipitation, polyethylene glycol (PEG) transformation, heat shock, lipofection, microinjection, and viral-mediated nucleic acid transfer. F&R Ref No.: 09531-0556WO1 Nucleic acids and the encoded polypeptide can be “endogenous” or “exogenous” to a host cell (e.g., a plant cell). An endogenous sequence refers to a sequence that originates in the host cell (e.g., within the genome of the host cell), whereas an exogenous sequence refers to a sequence that is not from the host cell and that is introduced into the host cell. Nucleic acids can be detected using any number of amplification techniques (see, e.g., PCR Primer: A Laboratory Manual, 1995, Dieffenbach & Dveksler, Eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; and U.S. Patent Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188) with an appropriate pair of oligonucleotides (e.g., primers). A number of modifications to the original PCR are known in the art and can be used to detect a nucleic acid. Nucleic acids also can be detected using hybridization. Hybridization between nucleic acids is discussed in detail in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Sections 7.37-7.57, 9.47-9.57, 11.7-11.8, and 11.45-11.57). Sambrook et al. discloses suitable Southern blot conditions for oligonucleotide probes less than about 100 nucleotides (Sections 11.45-11.46). The Tm between a sequence that is less than 100 nucleotides in length and a second sequence can be calculated using the formula provided in Section 11.46. Sambrook et al. additionally discloses Southern blot conditions for oligonucleotide probes greater than about 100 nucleotides (see Sections 9.47-9.54). The Tm between a sequence greater than 100 nucleotides in length and a second sequence can be calculated using the formula provided in Sections 9.50-9.51 of Sambrook et al. The conditions under which membranes containing nucleic acids are prehybridized and hybridized, as well as the conditions under which membranes containing nucleic acids are washed to remove excess and non-specifically bound probe, can play a significant role in the stringency of the hybridization. Such hybridizations and washes can be performed, where appropriate, under moderate or high stringency conditions. For example, washing conditions can be made more stringent by decreasing the salt concentration in the wash solutions and / or by increasing the temperature at which the washes are performed. In addition, interpreting the amount of hybridization can be affected, for example, by the specific activity of the labeled oligonucleotide probe, by the number of probe- binding sites on the template nucleic acid to which the probe has hybridized, and by the F&R Ref No.: 09531-0556WO1 amount of exposure of an autoradiograph or other detection medium. It will be readily appreciated by those of ordinary skill in the art that although any number of hybridization and washing conditions can be used to examine hybridization of a probe nucleic acid molecule to immobilized target nucleic acids, it is more important to examine hybridization of a probe to target nucleic acids under identical hybridization, washing, and exposure conditions. A nucleic acid molecule is deemed to hybridize to a nucleic acid but not to another nucleic acid if hybridization to a nucleic acid is at least 5-fold (e.g., at least 6- fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, or 100-fold) greater than hybridization to another nucleic acid. The amount of hybridization can be quantitated directly on a membrane or from an autoradiograph using, for example, a PhosphorImager or a Densitometer (Molecular Dynamics, Sunnyvale, CA). Polypeptides can be detected using antibodies. Techniques for detecting polypeptides using antibodies include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence. An antibody can be polyclonal or monoclonal. An antibody having specific binding affinity for a polypeptide can be generated using methods well known in the art. The antibody can be attached to a solid support such as a microtiter plate using methods known in the art. In the presence of a polypeptide, an antibody-polypeptide complex is formed. Detection (e.g., of an amplification product, a hybridization complex, or a polypeptide) is usually accomplished using detectable labels. The term “label” is intended to encompass the use of direct labels as well as indirect labels. Detectable labels include enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Modified Plants and Methods of Making Hybrids, varieties, lines, or cultivars are provided herein that have been modified to disrupt or knock-out one or more nucleic acids described herein (e.g., SEQ ID NOs: 96 and / or 101). In addition, hybrids, varieties, lines, or cultivars are provided herein that have been modified to overexpress one or more nucleic acids described herein (e.g., SEQ ID NOs: 94 and / or 95). As described herein, plants having one or more of the modifications described herein can exhibit an increase in seed size compared to a corresponding plant lacking the one or more modifications. F&R Ref No.: 09531-0556WO1 One or more of the sequences described herein can be disrupted, for example, by introducing one or more mutations into the sequence. Therefore, modified plants are provided in which a nucleic acid molecule described herein (e.g., SEQ ID NOs: 96 and / or 101) has been disrupted. As discussed herein, a disruption in a nucleic acid sequence can be a point mutation, an insertion, a deletion, a substitution, or combinations thereof. For example, a mutation in a promoter sequence can alter or eliminate the binding or recognition site of a transcription factor or of the polymerase enzyme, or a mutation in a promoter sequence can alter or eliminate the function of an enhancer, an activator or the like, or a repressor, a silencer or the like. Mutations in a promoter sequence can result in altered or absent transcription, or production of a less-than-functional or non-functional transcript from improper expression (e.g., expressed in the wrong place or at the wrong time) or from degradation of the transcript. Insertion, deletion or substitution of one or more amino acids in a coding sequence, for example, can disrupt the conformation of the encoded polypeptide, thereby disrupting sites important for recognition of a binding ligand or for activity of the polypeptide. In addition, one or more mutations can introduce a stop codon to produce a truncated polypeptide, or disrupt an active site or domain (e.g., a catalytic site or domain, a binding site or domain) within the polypeptide. In addition, mutating a target sequence or a cleavage motif can alter the location of a polypeptide. In addition to mutation, another way in which expression of one or more sequences can be disrupted (e.g., reduced or knocked-out) is to use inhibitory RNAs (e.g., RNAi). RNAi technology is known in the art and is a very effective form of post- transcriptional gene silencing. RNAi molecules typically contain a nucleotide sequence (e.g., from about 18 nucleotides in length (e.g., about 19 or 20 nucleotides in length) up to about 700 nucleotides in length) that is complementary to the target sequence in both the sense and antisense orientations. The sense and antisense strands can be connected by a short “loop” sequence (e.g., about 5 nucleotides in length up to about 800 nucleotides in length) and expressed in a single transcript, or the sense and antisense strands can be delivered to and expressed in the target cells on separate vectors or constructs. A number of companies offer RNAi design and synthesis services (e.g., Life Technologies, Applied Biosystems). Therefore, transgenic plants are provided that contain a transgene encoding at least one RNAi molecule, which, when expressed, silences at least one of the endogenous nucleic acids described herein (e.g., SEQ ID NOs: 96 or 101). As described F&R Ref No.: 09531-0556WO1 herein, such transgenic plants exhibit an increase in seed size (e.g., compared to a plant lacking or not expressing the RNAi). One or more of the sequences described herein can be overexpressed in plants. Therefore, transgenic plants are provided that are transformed with a nucleic acid molecule described herein (e.g., SEQ ID NOs: 94 and / or 95) under control of a promoter that is able to drive expression in plants (e.g., a plant promoter). As discussed herein, a nucleic acid molecule used in a plant expression vector can have a different sequence than a sequence described herein, which can be expressed as a percent sequence identity or based on the conditions under which sequences hybridize. As an alternative to using a full-length sequence, a portion of the sequence can be used that encodes a polypeptide fragment having the desired functionality, referred to herein as a “functional fragment.” When used with respect to nucleic acids, it would be appreciated that it is not the nucleic acid fragment that possesses functionality but the encoded polypeptide fragment. Methods of introducing a nucleic acid (e.g., an exogenous nucleic acid) into plant cells are known in the art and include, for example, particle bombardment, Agrobacterium-mediated transformation, microinjection, polyethylene glycol-mediated transformation (e.g., of protoplasts, see, for example, Yoo et al. (2007, Nature Protocols, 2(7):1565-72)), liposome-mediated DNA uptake, or electroporation. Following transformation, the transgenic plant cells can be regenerated into transgenic plants. As described herein, expression of the transgene results in plants that exhibit an increase in seed size, relative to a plant not expressing the transgene. The regenerated transgenic plants can be screened for seed size compared to a corresponding non-transgenic plant, and can be selected for use in, for example, a breeding program as discussed herein. Following modification (e.g., disrupting AGL9 and / or AGL15 with or without overexpressing ARR11 and / or SHB1), plants can be regenerated from the cells and those plants, or a subsequent generation of that population, can be crossed, if necessary, and screened for one or more of the modifications described herein. Screening for plants having one or more of the modifications described herein can be performed using methods routine in the art (e.g., hybridization, amplification, combinations thereof) or by evaluating the phenotype of the plants (e.g., seed size compared to a corresponding plant (e.g., having the same varietal background) lacking the modification(s) grown under corresponding conditions). F&R Ref No.: 09531-0556WO1 As used herein, seed size typically refers to the average seed size of 100 count seeds. Average seed size can refer to, e.g., average length, average width, average height, average seed weight, or a combination thereof. As used herein, an “increase” in seed size refers to a statistically significant increase in seed size by at least about 50% up to about 200% (e.g., about 60% to about 175%, about 75% to about 150%, about 100% to about 150%, about 110% to about 140%, about 120% to about 130%) relative to seed size from a corresponding plant lacking the modification(s) and grown under corresponding conditions. It would be appreciated that an increase (e.g., a statistically significant increase) in seed size typically also correlates with an increase in the amount of oil in the seed. As used herein, statistical significance refers to a p-value of less than 0.05, e.g., a p- value of less than 0.025 or a p-value of less than 0.01, using an appropriate measure of statistical significance, e.g., a one-tailed two sample t-test. Following modification, the modified plant cells can be regenerated into modified plants, which can be screened for seed size, and plants having increased seed size compared to seed size in a corresponding non-modified plant can be selected and used, for example, in a breeding program as discussed herein to create novel and useful cultivars, lines, varieties and hybrids. Thus, in some embodiments, a plant containing at least one modification (e.g., overexpression and / or disruption) is crossed with a second plant, and progeny of the cross are identified in which the modification(s) is present. It will be appreciated that the second plant can contain the same modification(s) as the plant to which it is crossed, one or more different modification(s), or be wild type at the locus. Additionally or alternatively, a second plant can exhibit a particular desirable phenotypic trait such as, for example, disease resistance, high yield, leaf quality, height, plant maturation, stalk size, and / or leaf number per plant. Breeding can be carried out using known procedures. DNA fingerprinting, SNP or similar technologies can be used in marker-assisted selection (MAS) breeding to transfer or breed modifications into other lines, varieties or cultivars. Progeny of the cross can be screened for one or more modifications using methods described herein, and plants having one or more modifications as described herein can be selected. For example, plants in the F2 or backcross generations can be screened using a marker developed from a sequence described herein or a fragment thereof using one of the techniques listed herein. Plants also can be screened for seed size (e.g., average seed size), and those plants having increased seed size compared to a corresponding plant that lacks the one or more F&R Ref No.: 09531-0556WO1 modifications can be selected. Plants identified as possessing the one or more modifications and / or the appropriate phenotype (i.e., increased average seed size) can be backcrossed or self-pollinated to create a second population to be screened. Backcrossing or other breeding procedures can be repeated until the desired phenotype of the recurrent parent is recovered. Successful crosses yield F1 plants that are fertile and that can be backcrossed with one of the parents if desired. In some embodiments, a plant population in the F2 generation is screened for the variant gene expression (e.g., overexpression or disruption) using standard methods (e.g., PCR with primers based upon the nucleic acid sequences disclosed herein). Selected plants then can be crossed with one of the parents and the first backcross (BC1) generation plants can be self-pollinated to produce a BC1F2 population that again can be screened for variant gene expression. The process of backcrossing, self- pollination, and screening can be repeated, for example, multiple times until the final screening produces a plant that is fertile and reasonably similar to the recurrent parent. Breeder’s seed of the selected plant can be produced using standard methods including, for example, field testing, genetic analysis, and / or confirmation of the phenotype. The result of a plant breeding program using the modified plants described herein are novel and useful cultivars, varieties, lines, and hybrids. As used herein, the term “variety” refers to a population of plants that share constant characteristics which separate them from other plants of the same species. A variety is often, although not always, sold commercially. While possessing one or more distinctive traits, a variety is further characterized by a very small overall variation between individual with that variety. A “pure line” variety may be created by several generations of self-pollination and selection, or vegetative propagation from a single parent using tissue or cell culture techniques. A “line,” as distinguished from a variety, most often denotes a group of plants used non-commercially, for example, in plant research. A line typically displays little overall variation between individuals for one or more traits of interest, although there may be some variation between individuals for other traits. The methods described herein can be used with any number of plants including, without limitation, Camelina, pennycress, canola or soybean. Depending on the plant species, hybrids can be produced by preventing self- pollination of female parent plants (i.e., seed parents) of a first variety, permitting pollen from male parent plants of a second variety to fertilize the female parent plants, and F&R Ref No.: 09531-0556WO1 allowing F1 hybrid seeds to form on the female plants. Self-pollination of female plants can be prevented by emasculating the flowers at an early stage of flower development. Alternatively, pollen formation can be prevented on the female parent plants using a form of male sterility (e.g., cytoplasmic male sterility (CMS), nuclear male sterility, genetic male sterility, molecular male sterility where a transgene inhibits microsporogenesis and / or pollen formation, or self-incompatibility). In embodiments in which the female parent plants are CMS, the male parent plants typically contain a fertility restorer gene to ensure that the F1 hybrids are fertile. In other embodiments in which the female parents are CMS, male parents can be used that do not contain a fertility restorer. F1 hybrids produced from such parents are male sterile. Male sterile hybrid seed can be interplanted with male fertile seed to provide pollen for seed-set on the resulting male sterile plants. Embodiments Embodiment 1 is a modified oilseed plant exhibiting increased seed size and seed yield relative to a corresponding non-modified oilseed plant, wherein the modified oilseed plant comprises an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide. Embodiment 2 is the modified oilseed plant of Embodiment 1, wherein the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:113. Embodiment 3 is the modified oilseed plant of Embodiment 1 or 2, wherein the modified oilseed plant comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111. Embodiment 4 is the modified oilseed plant of Embodiment 3, wherein the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:111. Embodiment 5 is the modified oilseed plant of Embodiment 1 or 2, wherein the modified oilseed plant further comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112. Embodiment 6 is the modified oilseed plant of Embodiment 5, wherein the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:112. F&R Ref No.: 09531-0556WO1 Embodiment 7 is the modified oilseed plant of any one of Embodiments 1-6, wherein the modified oilseed plant further comprises an endogenous nucleic acid encoding an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:114, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL15 polypeptide. Embodiment 8 is the modified oilseed plant of Embodiment 7, wherein the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:114. Embodiment 9 is the modified oilseed plant of any one of Embodiments 1-8, wherein the oil seed plant is selected from Camelina, pennycress, canola or soybean. Embodiment 10 is a method of increasing seed size and seed yield in an oil seed plant, comprising: disrupting expression of a first endogenous nucleic acid molecule in cells from the oil seed plant, wherein, prior to disrupting, the first endogenous nucleic acid molecule encodes an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the oil seed plant expresses little to no AGL9 polypeptide. Embodiment 11 is the method of Embodiment 10, wherein expression of the first endogenous nucleic acid molecule in the cells from the oil seed plant is disrupted using gene editing. Embodiment 12 is a method of Embodiment 10 or 11, wherein the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:113. Embodiment 13 is the method of any one of Embodiments 10-12, further comprising: introducing a first exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the first exogenous nucleic acid molecule encodes an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111. Embodiment 14 is the method of Embodiment 13, wherein the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:111. Embodiment 15 is the method of any one of Embodiments 10-12, further comprising: introducing a second exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the second exogenous nucleic acid molecule encodes an SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112. F&R Ref No.: 09531-0556WO1 Embodiment 16 is the method of Embodiment 15, wherein the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:112. Embodiment 17 is the method of any one of Embodiments 10-16, further comprising: disrupting expression of a second endogenous nucleic acid molecule in the cells from the oil seed plant, wherein, prior to disrupting, the second endogenous nucleic acid molecule encodes an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:114. Embodiment 18 is the method of Embodiment 17, wherein the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:114. Embodiment 19 is the method of any one of Embodiments 10-18, wherein the oil seed plant is selected from Camelina, pennycress, canola or soybean. Embodiment 20 is the method of any one of the Embodiments 10-19, wherein expression and / or activity of endogenous MINI3 and / or endogenous IKU2 is / are increased in the oil seed plant. Embodiment 21 is a method of increasing seed size and seed yield in an oil seed plant, comprising: a) providing a first modified oilseed plant, wherein the modified oilseed plant comprises an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide; b) providing a second modified oilseed plant, wherein the second modified oilseed plant: i) comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111, or ii) comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112; and c) crossing the first modified plant with the second modified plant to produce progeny plants, wherein the progeny plants exhibit increased seed size and seed yield. Embodiment 22 is the method of Embodiment 21, wherein the first and the second oilseed plants are selected from Camelina, pennycress, canola or soybean. In accordance with the present invention, there may be employed molecular biology, microbiology, biochemical, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. The invention will be further F&R Ref No.: 09531-0556WO1 described in the following examples, which do not limit the scope of the methods and compositions of matter described in the claims. EXAMPLES Experimental Overview We created large seed cultivars using two alternative strategies followed by greenhouse and field trials. First, we promoted endosperm proliferation by overexpressing two endosperm proliferation genes and, second, we prolonged endosperm proliferation by editing a suppressor of endosperm proliferation. Camelina is readily transformable by Agrobacterium infiltration, which generates stable lines. Our data suggest that both strategies are successful in the spring cultivar, Suneson. Transgenic seedlings from the facultative cultivar and the winter cultivar have been grown. As described below, we introduced Arabidopsis ARR11 and SHB1 sequences into the Camelina spring variety, Suneson. Several transgenic lines showed a large seed phenotype (FIG.1). Both genes were driven by their own promoters to ensure the spatial and temporal expression pattern of each gene. The growth and development of ARR11 or SHB1 overexpression seedlings and adult plants were like that of wild type Camelina. Experiments were performed with two winter cultivars, one that has a facultative requirement for vernalization and the other that is a true winter cultivar. The winter cultivars flower and produce seeds in late spring, allowing the growth of many other crops such as corn and soybean in late spring throughout the summer. We designed a single gRNA (CAA GCT TTC TTC CAG CCT TTG G (SEQ ID NO:120)) against the second exon from the stop codon for all three Camelina AGL9. Editing AGL9 alone in Camelina Suneson produced large seeds (FIG.1). These results suggest that editing of AGL9 alone is sufficient to engineer a cultivar that produces large seed. The transgenic plants were examined for gene editing and DNA was prepared from wild type, line 4 that had no seed phenotype, and line 10 that had a large seed phenotype. By definition, T0 transgenic plants after transformation and antibiotic selection produce T1 seeds. The DNA was prepared from T1 seedlings that germinated from the T1 seeds. Their genome has been edited once, since the gRNA is driven by an egg-specific promoter. We first used a U6-26p-F primer and a U6-26t-R primer to amplify a 423 bp fragment from the editing cassette that was integrated into the plant genome to confirm the presence of the transgene. F&R Ref No.: 09531-0556WO1 The gRNA contains a BslI enzyme restriction site, CCN NNN NNN GG where editing mostly occurs. The enzyme only cuts the unedited wild type DNA. We designed three unique PCR primers to amplify the three different fragments. Csa3g 9N5 GCT AGC TAG CTA GGT GTA CA (SEQ ID NO:121) and Csa3g / 9 RP AAT AGA GTT GGT ATC ATA AGG (SEQ ID NO:122) amplify an 878 bp fragment. BslI digestion generates 628 bp and 250 bp fragments for unedited locus. Csa14g 9N5 TAA CGA AGC AAG TAC TAC TG (SEQ ID NO:123) and Csa14g / 9 RP TAT AGA GTT GGT ATC ATA AGG TAA C (SEQ ID NO:124) amplify a 402 bp fragment. If it is not edited, 153 bp and 249 bp fragments should be observed after restriction digestion. Csa17g 9N5 ACT CAC TAA TAT CTA GCT CC (SEQ ID NO:125) and Csa17g / 9 RP AAT AGA GTT GGT ATC GTA AGG (SEQ ID NO:126) amplify a 579 bp fragment and restriction digestion generates 313 bp and 266 bp fragments. In line 10, Csa03g030490 was not edited, Csa14g034830 was edited to homozygosity, and Csa17g035980 was edited to heterozygosity. No editing was observed in line 4 that has no seed phenotype. Two winter cultivars are gene edited as described above. The selected T0 transgenic lines are examined for seed size phenotype in T1 transgenic seeds. Similar experiments are performed for early detection of gene editing. The plants also are propagated to T2 generation, allowing another round of gene editing followed by seed size assessment. Once the transgenic plants are produced, an ARR11:MYC transgenic line are crossed to a SHB1:FLAG transgenic line or the AGL9 cr lines. ARR11 and SHB1 polypeptides work together, so overexpression of both ARR11 and SHB1 genes or overexpression of ARR11 or SHB1 with AGL9 cr knockout result in the production of large seeds. The engineered cultivars are examined for mature seed size and yield under conditions mimicking the ambient and seasonal light and temperature regimes in the greenhouse. Following the greenhouse experiments, field trials are conducted with engineered Camelina cultivars. Ultimately, engineered winter cultivars with increased seed yield and oil contents are provided. Example 1—ARR11 and SHB1 and their Role in Seed Size in Oilseed Plants Transcription factor, ARR11, recruits SHB1 to a number of key endosperm proliferation genes (e.g., MINI3 and IKU2). We overexpressed ARR11 in Arabidopsis. F&R Ref No.: 09531-0556WO1 Seed mass produced from these various plants are shown in FIG.2, FIG.3 and FIG.4. FIG.2 shows the seed mass in Col ecotype, arr11 cr mutant, two ARR11 overexpression lines in Col, Ws ecotype, ARR11 CRES-T knockdown line, two ARR11 overexpression lines in Ws background, and shb1-D as a positive control. FIG.3A shows three additional ARR11 overexpression lines in Col ecotype, while FIG.3B shows three ARR11 overexpression lines in Camellia sunesun cultivar. Example 2—Plant Materials and Growth Conditions Arabidopsis thaliana ecotype Columbia-0 (Col-0), Landsberg erecta (Ler), and Wassilewskija (Ws) were used as Arabidopsis wide types. Arabidopsis mutant lines agl9- 1 (SALK_065223), agl15-2 (SALK_093946), and agl15-3 (SALK_076234) were acquired from ABRC. Arabidopsis mutant line medea-3 was kindly provided by Dr. Yadegari (Kiyosue et al., 1999). All Arabidopsis plants were grown under a photoperiod of 16 h of light and 8 h of dark at 22°C and 60% relative humidity. Example 3—Plasmid Construction and Generation of Transgenic Plants Various MEA, AGL9, and AGL15 genes driven by their native promoters were PCR-amplified from Col-0 genomic DNA and cloned into the pCRTM8 / GW / TOPO®TA Cloning entry vector. MEA promoter was 812 bp from -812 to -1, AGL9 promoter was 1543 bp from -1543 to -1, and AGL15 promoter was 1259 bp from -1259 to -1. The MEA TA fragment was recombined into the pEARLYGATE303 vector to create a MYC fusion construct. The genomic region of MEA with its native promoter was also PCR-amplified and cloned into the binary vector pSPYNE to create a YFPNfusion construct (Walter et al., 2004). The AGL9 and AGL15 TA fragments were recombined into the pEARLYGATE302 and pMDC107, respectively, vectors to create FLAG and GFP fusion constructs. All stable Arabidopsis transgenic plants were created by the floral dip method with Agrobacterium tumefaciens GV3101. For AGL9 CRISPR-Cas9 knockout, we annealed two sgRNA oligos against the AGL9 N-terminus and C-terminus. The gRNAs were evaluated for target specificities by potential off-target finder (rgenome.net / cas-offinder / on the World Wide Web) and genome-wide prediction of plant CRISPR / Cas9 target (genome.arizona.edu / crispr / CRISPRsearch.html on the World Wide Web). All gRNAs used were not off-target by design. The sgRNA oligos were cloned into the pHEE401E F&R Ref No.: 09531-0556WO1 vector (Wang et al., 2015). The correct clones were identified by colony PCR and verified by sequencing. The binary vectors were transformed into the Agrobacterium tumefaciens GV3101 strain and introduced to Arabidopsis by floral dip. The selection marks were kanamycin in E. coli and hygromycin in plants. For N-terminal AGL9 edit, the genomic region was PCR-amplified with AGL9-5 and AG960-3 primers and digested with the restriction enzyme HpyAV. The C-terminal edited AGL9 regions were PCR-amplified with AG9 cc5 and AGL9c3 primers and digested with the restriction enzyme EarI. Genomic fragments in homozygous editing lines were finally PCR-amplified and sequenced for lesions. All primers are listed in Table 1. Arabidopsis ARR11:Myc is introduced into enlarged camelina mature seeds from the Camelina Suneson variety by Agrobacterium infiltration. We choose Suneson variety since it has high oil content and also grows better than other varieties in marginal lands. ARR11:Myc is driven by its native promoter with a hygromycin selection marker. The native promoters ensure its spatial and temporal expression pattern. The Suneson transgenic lines that exhibit a large seed phenotype are characterized for transgene expression and protein accumulations. SHB1 driven by its own promoter is overexpressed with a Flag tag and a basta selection marker in one of the camelina ARR11:Myc overexpression lines generated above. Simultaneous overexpression of both ARR11 and SHB1 genes driven by their own promoters produced even larger seeds in Arabidopsis. Several SHB1:Flag transgenic lines are generated with gene expression ranging from moderate to strong. The lines are further characterized by transgene expression and protein accumulations. The selected transgenic lines are propagated to homozygosity at T3 generation and examined for seed size phenotype. The two CsaAGL9s in camelina are knocked-out using the Crispr-Cas system. We have designed gRNAs that target either N-terminal or C-terminal exons of CsaAGL9-1 and CsaAGL9-2. The gRNAs have been evaluated for target specificities to avoid off-target on several websites. We have introduced the Crispr-Cas vectors to Camelina Suneson variety by Agrobacterium infiltration. T2 transgenic seeds are plated in hygromycin medium for selection of single transgene insertion lines. For all single- insertion lines, the modification of the target genes near the PAM and / or gRNA site are monitored through PCR and restriction digestion. The edits are brought to homozygosity at T3 generation and sequenced to identify the molecular lesions. Several independent homozygous lines are examined for seed size phenotype. F&R Ref No.: 09531-0556WO1 An exon near the CsaAGL15 C-terminus is edited in Csaagl9s mutant background generated above. In Arabidopsis, AGL9 N-terminal edit in either agl15-2 or agl15-3 background fails to deliver homozygous lines. We have identified unique gRNA sequences against a CsaAGL15 C-terminal exon with an adjacent PAM sequence. The Crispr-Cas vectors are introduced to Csaagl9s by Agrobacterium infiltration. T2 transgenic seeds are plated in hygromycin medium for selection of Crispr-Cas single insertion lines. The modification of the target genes is monitored with T2 siliques through PCR and restriction digestion. Several independent homozygous lines are examined for seed size phenotype. Example 4—RNA Extraction and qRT-PCR Analysis Total RNAs were isolated from developing siliques at 4 to 5 DAP using the GeneJET RNA Purification Mini Kit (Thermo Scientific™). One µg of total RNA was used for the first-strand cDNA synthesis with the SuperScript III reverse transcriptase kit (Invitrogen). qRT-PCR was performed with the SYBR®Premix Ex TaqTMII (Takara) on a CFX Duet Real-Time PCR System (Bio-Rad). Data were generated from three biological replicates and each biological replicate was represented by two technical replicates. The primers used for qRT-PCR were listed in Table 1. Table 1. Primers used in this study. Primer name Sequence (5’ to 3’) SEQ ID NO: Primers for qRT-PCR IKU2R15TTGATCTCGACGACGTTT1iku2 / 3ATCTGACCACGTAAAGAGTT2Mini3 / 5nCAAAGATGATGACGACGAGG3mini3 / 3867TGATCCTTTGTGTCTTGCTT4MEA RT5CAGCTCGAAATCGATGCT5MEA CDS 3ACGAGCTGGACGGGCTTC6AGL9-5ATGGGAAGAGGGAGAGTA7AG9 60-3ACTACTGCAAAACTCGTA8AGL15-5ATGGGTCGTGGAAAAATCG9AGL15 84-3ACAATCCTCCTCTGCTTT10AT1G69690 FCTCCTAAACGAACCTCTA11AT1G69690 RTGGAGTAGCCACTCAATA12T2G35940 FTTACTTTCACGGAAACCC13T2G35940 RCGAGGAAAACGAAACTAC14AT2G42730 FTCTCGCATTCAAAGTTGG15AT2G42730 RGGAAGAGAAACATCTTGAGA16AT5G43270 FACCGTTTCAATGGGAATT17AT5G43270 RCTTCAGCTGATGAAGAGC18 F&R Ref No.: 09531-0556WO1AT5G55080 FGCTTTACCTAACCAACAAAA19AT5G55080 RGTATTATGCTCAAATTCCCC20AT5G65310 FACAAATAAGCCCAAGACC21AT5G65310 RCCTCTCTGGCTCTAACTT22Actin N5TATTGTGCTGGATTCTGGT23Actin 3NGGAGAGCTTCTCCTTGATG24UBQ10-5CAGGATAAGGAGGGCATT25UBQ10 R246GTCTTTCCCGTTAGGGTT26Primers for Y1HIK B2UCCTTCTTATTTTGGAAACTTCTTATT27 TTGGAAACTTCTTATTTTGGAAACIK B2LTCGAGTTTCCAAAATAAGAAGTTTCC28 AAAATAAGAAGTTTCCAAAATAAGAA GGGTACIK B2UmCCTTATTATTTTATAAACTTATTATT29 TTATAAACTTATTATTTTATAAACIK B2LmTCGAGTTTATAAAATAATAAGTTTAT30 AAAATAATAAGTTTATAAAATAATAA GGGTACM3 B4triUCAAACAAAATTTGGAAAAAACAAAAT31 TTGGAAAAAACAAAATTTGGAAACM3 B4triLTCGAGTTTCCAAATTTTGTTTTTTCC32 AAATTTTGTTTTTTCCAAATTTTGTT TGGTACM3 B4triUmCAAATAAAATTTATAAAAAATAAAAT33 TTATAAAAAATAAAATTTATAAACM3 B4triLmTCGAGTTTATAAATTTTATTTTTTAT34 AAATTTTATTTTTTTAAAATTTTATT TGGTAC Primers for Y2HMEA cDNA CDS 5ATGGAGAAGGAAAACCATG35MEA CDS 3ACGAGCTGGACGGGCTTC36MEA 406-3GGTAACCTGATTGTGTCT37MEA 401-5ATGAGACACAATCAGGTTACC38AGL9-5ATGGGAAGAGGGAGAGTA39AGL9-3TAACAATGCTCACTGCATGG40AG9 60-3ACTACTGCAAAACTCGTA41AG9 95-3CTGGCTACTAAGTTCAAC42AG9 172-3TCTTAGAGTTTTATTTGT43AG9 170-5CTAAGACTAAGGTTAGCT44AGL15-5ATGGGTCGTGGAAAAATCG45AGL15 c3AGAGAACCTTTGTCTTTTGGC46AGL1584-3ACAATCCTCCTCTGCTTT47AGL15150-3TTCCTTGAGGCGTGATTC48Primer for ChIP q-PCRpIK35 (for box 1)GGTACCTACGTACGTGTTGGTGGT49pIK33CTCGAGGGAGGGTATGTAAATATG50IKU2 P1 / 5 (for box 2)TCTCCGGTCTCTCTTGATAA51IK2 AGL3CTCGAGCTTGAATCATATCCGTTGG52pIK15 (for box 3)GGTACCATGCTGATGCAAACGTGT53IKU2 P2 / 3TCTCTACGTCGGAAGGATTA54IKU2R15TTGATCTCGACGACGTTT55 F&R Ref No.: 09531-0556WO1 iku2 / 3ATCTGACCACGTAAAGAGTT56pM3 nu5 (for box 1)GGTACCCGTCCAAGCGATAGCTTT57M3 nu3 (124-142)CCGGAGTTAAACTAGATTG58MINI3 P3 / 3 (for box 2)TTGGTTGGACTGGTAGAGTCAG59MINI3 P3 / 5TGATGGTATAGTACCGTGATCG60pM3l 5 (for box 3)GGTACCCCCAATCACATTGAAGTT61MINI3 P2 / 5TTGTTTTCAATTTTTCACAT62MINI3 P1 / 3 (for box 4)AACCGAAGTAGAAACCTAAA63MIN3 / 1306GAGGAATATAGTGGGTCT64Mini3 / 5nCAAAGATGATGACGACGAGG65mini3 / 3867TGATCCTTTGTGTCTTGCTT66Primers for gene cloning AGL9 p5GAGACCATGACCAAGTGA67AGL9 c3AGAGTTGGTGTCATAAGG68AGL15 p5AGAAGCATGGAACAGTCG69AGL15 C3AGAGAACCTTTGTCTTTTGGC70MEA P5GATATTTGACATATTATACTCATC71MEA CDS 3ACGAGCTGGACGGGCTTC72Primers for T-DNA genotyping LB5ACGGTTTTTCGCCCTTTG73AGL9-5TAACAATGCTCACTGCATGG74AGL9-3TAACAATGCTCACTGCATGG75AGL15-5TAACAATGCTCACTGCATGG76AGL15-3ATGCATATGACAATCGAATA77AGL15 150-3ATGCATATGACAATCGAATA78Primers for Crispr-Cas9 design and genotyping AGL9 nFATTGAGTGACGTTTGCAAAGAGA79AGL9 nRAAACTCTCTTTGCAAACGTCACT80AGL9 cFATTGCTGAACCCTAACCAAGAAG81AGL9 cRAAACCTTCTTGGTTAGGGTTCAG82AGL9-5AAACCTTCTTGGTTAGGGTTCAG83AG9 60-3AAACCTTCTTGGTTAGGGTTCAG84AGL9 cc5CACCAAATTAATGCATCAC85AGL9 c3AGAGTTGGTGTCATAAGG86Primers for AGL9, AGL15 and MEA association i55FTACACTAGATCGCTCGTC87AT1G69690 RTGGAGTAGCCACTCAATA88T2G35940 RCGAGGAAAACGAAACTAC89AT2G42730 RGGAAGAGAAACATCTTGAGA90AT5G43270 RCTTCAGCTGATGAAGAGC91AT5G55080 RGTATTATGCTCAAATTCCCC92AT5G65310 RCCTCTCTGGCTCTAACTT93Example 5—ChIP-PCR Arabidopsis siliques at 4 to 5 DAP were harvested, ground in liquid nitrogen, and fixed by 1% formaldehyde at 4^C for 10 min. Cross-linking was stopped by 2 M glycine F&R Ref No.: 09531-0556WO1 at 4^C for 5 min. After sonication, the chromatin complexes were incubated with a 1:1 ratio of monoclonal and polyclonal anti-GFP (MA5-15256, Thermo; A01388-40, Genscript) or anti-FLAG (MA1-91878, PA1-984B, Thermo) antibodies for 2 hr. Chromatin complexes incubated with BSA were used as negative controls. After reversal of the cross-linking and treatment with protein K, recovered DNA fragments were quantified by qPCR. All primers are listed in Table 1. Each amplicon was calculated using the following equation: 2-( Ct Fragment ChIP-Ct Fragment MOCK) / 2-(Ct ACTIN ChIP-Ct ACTIN MOCK)The fold of enrichment for various specific chromatin fragments was normalized to an enriched level of Arabidopsis ACTIN2 amplicon and to the negative control (BSA) of each fragment. About 200,000 sorted hexaploid endosperm nuclei were harvested by ConA beads and then fixed by 1% formaldehyde at 4^C for 10 min. Cross-linking was stopped by 2 M glycine at 4^C for 5 min. Liquid was carefully removed by pipette and a 0.4 ml nuclear lysis buffer was added to the tube for subsequent sonication. After sonication, the chromatin complexes were incubated with anti-H3K27me3 antibodies (Millipore 07-449) for 2 hr. Example 6—Yeast One-Hybrid Assays Yeast one-hybrid assays were performed for AGL9 and AGL15 in pGADT7 over trimeric repeats of wild-type or mutated IKU2 box 2 or MINI3 box 4 in a modified pLacZi vector (Lin et al., 2007; Wang et al., 2021). Each repeat of the element has the sequence with a 3-bp flanking sequence on either side of the core elements. Three tandem copies of the putative AGL9 and AGL15 binding elements were synthesized as oligonucleotides with end-incorporated Kpn I and Xho I restriction sites. Ten mM oligos were annealed at 95°C for 2 min, 72°C for 2 min, 37°C for 2 min, and 25°C for 2 min. One to two ml of oligos at 1 mM concentration were ligated into the Kpn I and Xho I sites of the modified pLacZi vector. The modified pLacZi vectors harboring the constructs were transformed into EYG48 cells. Yeast cells were grown on a minimal synthetic dropout (SD) medium lacking Ura. Full-length coding sequences of AGl9 and AGL15 were PCR-amplified from F&R Ref No.: 09531-0556WO1 cDNA generated from Arabidopsis Col-0 total RNA. All primers used were listed in Table 1. The PCR products were cloned into the pCRTM8 / GW / TOPO®TA Cloning entry vector. The cDNAs were then recombined into the GAL4-activation domain vector pDEST- GADT7. The EYG48 cells that harbored the derivative pLacZi vectors were transformed with GAD, GAD:AGL9, or GAD:AGL15 in pDEST-GADT7. Transformants were selected on SD medium lacking Leu and Ura. Yeast cells grown in SD / -Leu / -Ura broth were diluted to OD6000.4 and 4 ml was plated on SD / -Leu / -Ura media that contains BU salts at pH 7.25 (7.4 after autoclave) and 80 mg / ml X-gal (0.4 ml of 20 mg / ml X-gal in dimethylformamide per 100 ml). Images were photographed after 3 to 4 days. Example 7—Yeast Two-Hybrid Screens and Assays Full-length MEA coding sequence was PCR-amplified from cDNA generated from Arabidopsis Col-0 total RNA. The PCR product was cloned into the pCRTM8 / GW / TOPO®TA Cloning entry vector. The cDNA was then recombined into the GAL4-DNA-binding domain vector pDEST-GBKT7 and used for screen against a normalized Arabidopsis Mate and Plate library following the manufacturer’s instructions (Takara). The positive colonies were selected on SD / -Trp / -Leu / -His / -Ade medium at 30^C for three days. The cDNA clones of AGL9 and AGL15 were generated as described above. The cDNAs were then recombined into the GAL4-DNA-binding domain vector pDEST-GBKT7 or the GAL4-activation domain vector pDEST-GADT7. Both pDEST- GBKT7 and pDEST-GADT7 vectors were co-transformed into the yeast strain Y2H Gold by using the lithium acetate-based transformation protocol (Takara). The positive colonies were selected on the SD / -Trp / -Leu medium. The interaction assays were performed on selective SD / -Trp / -Leu / -His / -Ade medium at 30^C for three days. All primers used were listed in Table 1. Example 8—Bimolecular Fluorescence Complementation (BiFC) Assay To generate the BiFC constructs, cDNAs of MEA, AGL9, and AGL15 were PCR- amplified and cloned into binary vectors pSPYCE-35S and pSPYNE-35S, respectively, under the control of the cauliflower mosaic virus (CaMV) 35S promoter (Walter et al., 2004). pSPYNE::MEA was cotransformed with pSPYCE::AGL9 or AGL15 into N. benthamiana leaves by agroinfiltration together with a silencing suppressor P19 vector. Their interactions in N. benthamiana leaves were analyzed using an Olympus F&R Ref No.: 09531-0556WO1 fluorescence microscope (Olympus BX53 with a DP26 CCD camera) 2 to 3 days after the infiltration. Example 9—Protein Isolation and Immunoblot Total proteins were isolated from developing siliques at various DAP with RIPA buffer that contains 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 0.25% Na- deoxycholate, 1% Triton-100, 1 mM EDTA, 10% Glycerol, 14 mM β-mercaptoethanol, 1 mM PMSF, 1 mg / ml each of Aprotenin / Leupeptin / Pepstatin, and 5 mM benzylamidine. Forty ml protein extract was mixed with 10 ml 5× SDS buffer, boiled, and separated on 10% SDS-PAGE. MEA:MYC, AGL9:FLAG, AGL15:FLAG, AGL9:GFP and AGL15:GFP were detected in Western blots by using monoclonal anti-MYC (MA1- 21316, Thermo), polyclonal anti-FLAG (PA1-984B, Thermo) or polyclonal anti-GFP (A01388-40, Gencript) antibodies. Example 10—Co-IP Assay and Immunoblot Developing siliques of transgenic plants that carry either pMEA::MEA:MYC and pAGL9::AGL9:GFP or pMEA::MEA:MYC and pAGL15::AGL15:GFP at 4 to 5 DAP were used for Co-IP assays. Total proteins were isolated with a RIPA buffer minus 0.1% SDS. The protein extracts were centrifuged at 14,000 rpm for 20 min, and aliquots of the supernatants were incubated without or with polyclonal anti-GFP A01388-40 (Genscript) for 2 hr at 4°C and then with protein A / G agarose beads (Genscript) for another 2 hr at 4°C. After incubation, the beads were washed 3 times with the RIPA buffer without 0.1% SDS. Finally, proteins of 10% input, immunoprecipitation and a parallel immunoprecipitation were boiled in 20 ml 2× SDS buffer and separated on a single 8% SDS-PAGE. The Western blot was cut into three parts. The cut for input was probed with polyclonal anti-MYC A00172-40 (Genscript). The other two cuts from the two parallel immunoprecipitations were probed with monoclonal anti-MYC antibodies (MA1-21316, Thermo) and momoclonal anti-GFP antibodies (MA5-15256, Thermo), respectively. Example 11—AGL9:GFP and AGL15:GFP Detection Signals of AGL9:GFP and AGL15:GFP at 2 to 3 and 4 to 5 DAP were monitored in the integument and the endosperm by using iTOMEI procedure and confocal microscope (Sakamoto et al., 2022). The citation wavelength for GFP was 488 nm with a F&R Ref No.: 09531-0556WO1 confocal laser scanning microscope. Example 12—Silique and Seed Abortion Assays Silique abortion rates of various genotypes were determined for siliques born on inflorescence. Silique abortion was considered as the silique length less than one-third of the fully expanded siliques. Time course seed abortion was examined for fully expanded siliques from Col-0 and agl9 agl15-3 c3 primary inflorescence from 2 to 6 DAP. Seed abortion rates of various genotypes were then determined at 5 to 6 DAP. Example 13—Differential Interference Contrast (DIC) Microscopy and Cellularization Assay Developing seeds from 2 to 9 DAP were fixed in FAA (10% formalin, 5% acetic acid, 45% ethanol, and 0.01% Triton X-100) for 1 to 2 h. The developing seeds were then incubated in Visikol for Plant biology solution overnight (Visikol). The developing seeds from 5 to 9 DAP were cleared the second time with a modified Herr’s solution (10 mL of phenol, 10 mL of 85% lactic acid, 5 mL of xylene, 10 mL of clove oil and 10 mL of Visikol) for 2 to 3 hr. Cleared seeds were placed on a microscope slide, covered with several drops of Visikol for Plant Biology, and viewed under DIC optics using an Olympus BX51 microscope with an Olympus DP26 CCD camera (Waltham). The area of the endosperm was quantified by using NIH Image. For cellularization analysis, the siliques were peeled, and the seeds were incubated overnight in 4% glutaraldehyde fixative in 12.5 mM dimethyl arsenate buffer pH 6.9 (Liu et al., 2014). The samples were then washed three times in a PBS buffer for 5 min following the iTOMEI procedure (Sakamoto et al., 2022). The PBS buffer contains 8.1 mM Na2HPO4, 1.47 mM KH2PO4, 137 mM NaCl, and 2.68 mM KCl, pH of 7.4. The fixed samples were then treated with a decolorization solution for 24 h with gentle shaking in the dark. The decolorization solution contained 100 mM sodium phosphate buffer pH 8.0 with a mixture of 100 mM disodium hydrogen phosphate and 100 mM sodium dihydrogen phosphate at a ratio of 95:5 and 20% (w / v) caprylyl sulfobetaine. After being washed in PBS buffer for 5 min, the samples were incubated for 1 h with gentle shaking in the dark in serial mounting solutions of 20, 50, and 70.4% (w / w) iohexol (RI=1.52) in PBS buffer for 10 min each and in 70.4% (w / w) iohexol for 1 h. F&R Ref No.: 09531-0556WO1 Finally, the cleared seeds were mounted in 70.4% (w / w) iohexol in PBS buffer and observed with a confocal laser scanning microscope (Nikon A1si, Nikon), with the laser set to an excitation wavelength of 488 nm. Serial confocal optical sections are taken at a step size of 1.0 μm. Images are presented as a single section out of stacks of neighboring sections. Cellularization was quantified as the ratio of cellularized area over total endosperm area by using NIH Image. The maximum numbers of nuclei from 3 to 5 DAP were counted for an endosperm plane of the Z-stack images after the inner integument layer. Example 14—Rescue of agl9-1 or agl9 agl15 c1 Seed Phenotype by or line #14 was were genotyped by linked basta selection. agl9-1 and agl15-2 were genotyped by T-DNA left border and gene-specific primers. Edited AGL9 in agl9 agl15 c1 was genotyped by PCR and restriction digestion. Example 15—Library Preparation, Sequencing and Data Analysis of RNA-Seq Total RNAs were isolated from Col-0 or agl9 agl15-3 c3 developing seeds at 4 to 5 DAP using the Qiagen RNeasy Plant Mini Kit (Qiagen). The total RNA was then used for library preparation with the NEBNext Ultra II RNA Library Preparation kit for Illumina (NEB). Prepared mRNA libraries were pooled and sequenced with paired-end 150 on an Illumina HiSeq 2500 sequencing platform. Cutadapt was used to remove low-quality reads and to trim low-quality bases as well as adapters from the 150 bp paired-end RNA-seq reads. Trimmed reads were aligned to the TAIR10 genome via the Hitsat2 aligner. Alignments with low-quality mapping (MAPQ < 30) were filtered by using samtools (Li et al., 2009). The SAM alignment files were sorted and saved as BAM files. The BAM file was used to generate gene counts by using the htseq-count software. The EdgeR package was then used to determine the differential expression values between Col-0 and agl9 agl15-3 c3 mutant. The p-values were calculated based on the three biological replicates for each genotype. The list of significantly up-regulated genes was generated by selecting genes that were up-regulated at least two-fold (log2Fold > 1) in all three biological replicates with a p-value < 0.05. F&R Ref No.: 09531-0556WO1 The list of broadly up-regulated genes was generated by selecting genes that were upregulated at least two-fold (log2Fold > 1) in at least two out of the three biological replicates. Example 16—Isolation of Hexaploid Endosperm Nuclei and Low-Input CUT&Tag Arabidopsis siliques at 4 to 5 DAP from Col-0 or agl9 agl15-3 c3 were dissected under a light microscope. Developing seeds were brushed into a half strength MS liquid medium. Fresh seeds were ground manually in nuclei isolation buffer to extract nuclei by Partec CyStain UV Precise P kit (Sysmex). The nuclei were then stained by adding a nuclei staining buffer and were filtered through CellTrics 30 mm filter (Systmex). Nuclei with different DNA ploidy content were sorted by fluorescence-activated cell sorting (FACS) after DAPI staining (Zheng and Gehring 2019; Wu et al., 2022). Various peaks were indicated as 2C, 3C, 4C, and 6C by a BD FACSAria II flow cytometer (BD). About 50,000 sorted 6C nuclei were used for each H3K27me3 analysis experiment following the procedure of low-input nCUT&Tag (Ouyang et al., 2021) by using CUTANA™ pAG-Tn5 for CUT&Tag (EpiCypher) and anti-H3K27me3 antibodies (Millipore 07-449). The tagmented DNA was purified and dissolved in 30 ml of ddH2O. The sequencing library was prepared by using 6 ml of tagmented DNA in 50 ml PCR for 15 cycles with Q5 high-fidelity DNA polymerase (NEB). PCR-enriched library DNA was purified with AMPure XP beads. CUT&Tag libraries were pooled and sequenced with paired-end 150 on an Illumina HiSeq 2500 sequencing platform. Example 17—Data Analysis of CUT&Tag CUT&Tag data analysis was performed following the procedure by Zheng and Gehring (2019) prior to the peak calling step. Raw paired-end reads in CUT&Tag sequencing libraries were trimmed by Trimgalore for low-quality bases (quality value less than 20) and adapters to be at least 32 bp long. Trimmed reads were aligned to the TAIR10 genome using bowtie2 (in --local --very-sensitive mode) and SAM files were generated. Samtools was used to remove reads that were not uniquely mapped from further analysis (Li et al., 2009). After PCR duplicated reads were removed by Picard, bedtools were used to transfer and normalize the Sam file to bed, bigwig and bedGraph files for next-step analysis. SEACR (github.com / FredHutch / SEACR / on the World Wide Web; Meers et al.2019) was then used to call H3K27me3 broad peaks and calculate the F&R Ref No.: 09531-0556WO1 coverage value for each peak was calculated by using a pair of IgG control and H3K27me3 data in bedGraph format. The genomic loci of these broad peaks were identified and annotated from the TAIR10 gene annotation file using ChIPseeker, and the coverage value of each genomic loci was recalculated from broad peaks values. DeepTools was used to normalize the Bam files for the generation of the heatmap. The Integrative Genomics Viewer (IGV) genome browser was used to visualize the various peaks detected. The GO analysis of the functional category was performed by using AgriGO v2.0. Example 18—Promoter Element Analysis The 1000-bp upstream regions before the TSS site from the 35 identified target genes were used to perform motif enrichment analysis by PlantPAN 4.0 (plantpan.itps.ncku.edu.tw / plantpan4 / index.html on the World Wide Web). Arabidopsis transcription factor binding motif data is based on the PlantPAN 3.0 database. Fifty shuffled 1000-bp Arabidopsis genome sequences were used as reference sequences. Example 19—Association of AGL9:FLAG, AGL15:FLAG and MEA:YFPNwith Six Representative Loci Protocol of nCUT&Tag was used for AGL9:FLAG, AGL15:FLAG, and MEA:YFPNassociation analysis with the following modifications (Ouyang et al., 2021). Nuclei were isolated from 0.15 to 0.2 g developing siliques at 4 to 5 DAP from various transgenic plants (Saleh et al., 2008). The tissue was ground to fine powders in liquid nitrogen, added with a nucleus isolation buffer, and ground to mix the tissue and buffer until the lysates reached 4^C. The lysates were added with 1% formaldehyde and ground at 4^C for 10 min. Cross-linking was stopped by 2 M glycine at 4^C for 5 min. The lysates were centrifuged at 3,300 rpm for 10 min at 4^C to collect nuclei for the nCUT&Tag with a 1:1 ratio of monoclonal and polyclonal anti-FLAG (MA1-91878, PA1-984B, Thermo) or anti-GFP (MA5-15256, Thermo; A01388-40, Genscript) antibodies for 2 hr. The tagmented DNA was purified and dissolved in 30 ml of ddH2O. The nCUT&Tag library for qPCR analysis was prepared by using 3 µl of tagmented DNA in a 25 ml PCR reaction for 15 cycles with i5 and i7 primers and Q5 high fidelity DNA polymerase (NEB). PCR enriched library DNA is purified with AMPure XP beads and F&R Ref No.: 09531-0556WO1 dissolved in 30 ml of ddH2O. One ml was used for qPCR analysis with a 5’ primer derived from the i5 adaptor and 3’ genomic sequence-specific primers listed in Table 1. Example 20—Accession Numbers Sequence data can be found in the EMBL / GenBank data libraries under accession numbers At3G19700 (IKU2), AT1G55600 (MINI3), At1G02580 (MEA), AT1G24260 (AGL9), and AT5G13790 (AGL15). Example 21—AGL9, AGL15 and MEA Target the IKU2 and MINI3 Loci Critical for Endosperm Proliferation at 4 to 5 DAP IKU2 and MINI3 regulate Arabidopsis endosperm proliferation, and IKU2 or MINI3 mutations retard endosperm proliferation and reduce the size of mature seeds (Garcia et al., 2003; Luo et al., 2005). Both IKU2 and MINI3 were actively expressed at 2 to 3 DAP but repressed at 4 to 5 DAP. We examined the expression of IKU2 and MINI3 in mea mutant that was maintained as heterozygous MEA / mea. In general, 50% of the progeny seeds are genotyped as MEA / MEA and MEA / mea-3 (Kiyosue et al., 1999). Another 50% of the progeny are genotyped as mea / mea and mea / MEA, but the progenies were aborted since the paternal MEA allele is silenced or imprinted. After self-pollination of the MEA / mea-3 plants, we dissected siliques after 3 DAP and selected seeds that showed some of the endosperm developmental defects, such as the absence of cellularization, over-proliferation, and the presence of large nuclear clusters or nodules near the chalazal pole (Kiyosue et al., 1999; Luo et al., 2000; Wang et al., 2006). At 2 to 3 DAP, seeds of the mutant look very transparent under a microscope due to endosperm over-proliferation and accumulation of cytoplasmic fluid. By 4 to 5 DAP, the mutant seeds turn to a brownish color. However, we were unable to distinguish mea(matrenal) / mea(paternal) from mea(maternal) / MEA(paternal). Since the paternal MEA allele is silenced, they phenotypically look the same. The MEA / MEA seeds were taken from segregating seeds with wild type phenotype. The expression of IKU2 was still active in mea / mea and mea / MEA mutants at 4 to 5 DAP as shown previously (Wu et al., 2022). In addition to IKU2, the expression of MINI3 was also maintained in mea / mea and mea / MEA mutants at 4 to 5 DAP. PRC2 subunits do not bind DNA in a sequence-specific fashion. In a Y2H screen, we identified AGL9 and AGL15 with GBD:MEA as bait. We then searched for the F&R Ref No.: 09531-0556WO1 presence of any binding elements in either IKU2 or MINI3 promoter. Three CArG boxes were found in the IKU2 promoter, and four CArG boxes were found in the MINI3 promoter. MADS-box proteins bind the potential CArG-box sequence: 1 or 2 C followed by 6 to 8 A or T and then 1 or 2 G (Kaufmann et al., 2005). We next tested whether MEA, AGL9, and AGL15 associate in vivo with the regions surrounding the potential CArG- boxes. Through ChIP-qPCR experiments, MEA:YFPNwas predominantly associated with the IKU2 box 2 and MINI3 box 4 at 4 to 5 DAP but not at 2 to 3 DAP. AGL9:FLAG and AGL15:FLAG recognized the same regions. The CArG-boxes are CTTATTTTGG (SEQ ID NO: 109) in the IKU2 promoter and CAAAATTTGG (SEQ ID NO: 110) in the MINI3 promoter. Both AGL9 and AGL15 binding sites require 1 C at the 5’ but 2 G at the 3’. The expression of MEA:YFPN, AGL9:FLAG, and AGL15:FLAG transgenes driven by their own promoters were verified in several independent transgenic lines. To confirm a direct binding of AGL9 or AGL15 to IKU2 box 2 or MINI3 box 4, we performed Y1H assays with a trimer made of three monomeric box 2 or box 4 upstream of a LacZ gene in the pLacZi vector. GAD, GAD:AGL9 or GAD:AGL151-150 were then introduced to EYG48 yeast cells that have already harbored the pLacZi reporter. The IKU2 box 2 or MINI3 box 4 were also mutated with the C at the 5’ and 2 Gs at the 3’ replaced by A or T and AT. Either GAD:AGL9 or GAD:AGL15-150 bound wild type IKU2 box 2 and MINI3 box 4 but not the mutated IKU2 box 2 and MINI3 box 4. GAD:AGL15 is toxic to yeast cells and the transformation efficiency was extremely low for GAD:AGL15. In contrast, GAD:AGL15-150 is not toxic to yeast cells. Since the DNA binding domain lies in the N-terminus of AGL15, GAD:AGL15-150 was used for Y1H analysis. In summary, expression of IKU2 or MINI3 in Ler at 2 to 3 DAP was significantly different from that at 4 to 5 DAP by two-tailed Student’s t-test (p<0.01). At 4 to 5 DAP, expression of IKU2 and MINI3 in mea / mea and mea / MEA was significantly different from that in Col-0 by two-tailed Student’s t-test (p<0.01). Enrichment of IKU2 probe 2 and MINI3 probes 3 or 4 with antibody at 4 to 5 DAP was significantly different from that of – or + antibody at 2 to 3 DAP and - antibody at 4 to 5 DAP by two-tailed Student’s t- test (p<0.05 * and p<0.01 **). F&R Ref No.: 09531-0556WO1 Example 22—AGL9 and AGL15 Interact with and Recruit MEA to the IKU2 and MINI3 Loci If MEA associates with the IKU2 and MINI3 promoters through AGL9 and AGL15, MEA should directly interact with AGL9 and AGL15. MEA contains a SANT domain for SWI3, ADA2, N-CoR and TFIIIB DNA-binding domains from amino acid 339 to 389 (Boyer et al., 2004), It also contains a CXC domain with three units of C- X(6)-C-X(3)-C-X-C motif as a potential zinc binding domain from amino acid 430 to 543, and a SET domain for protein-protein interaction in some lysine methyltransferase enzymes from amino acid 543 to 663 (Boyer et al., 2004). The SET domain and the adjacent cysteine-rich regions on both sides of the SET domain are possibly essential for substrate recognition and histone methyltransferase activity (Yeates, 2002). In yeast two- hybrid assays, GBD:MEA interacted with GAD:AGL9 or GAD:AGL15. The MEA CXC domain appeared to play a major role in its interaction with AGL9 and a further truncation in the CXC domain from amino acid 513 to 689 diminished its interaction with AGL9. The MEA CXC plus SET domains were required for its interaction with AGL15 since a further truncation in the CXC domain from amino acid 513 to 689 still showed a weak interaction with AGL15. When fused with GBD, MEA N- terminus from amino acid 1 to 406 which contains the SANT domain caused a strong background growth. We therefore fused the MEA N-terminus with GAD and examined its interaction with GBD:AGL9 or GBD:AGL15. The MEA N-terminus did not interact with AGL9 but weakly with AGL15. MADS-box domain proteins of the plant-specific MIKC-type consist of four domains: MADS-box (M), intervening (I), keratin-like (K), and C-terminal (C) domains (Kaufmann et al., 2005). The MADS domain is highly conserved and involved in DNA binding and dimerization. The I-region is likely a linker between the MADS-box domain and the K-domain and may share the dimerization function with the MADS-box. The K- box is weakly conserved and interacts with other proteins. It resembles the structural features of the coiled-coil domain of Keratin with three consecutive amphipathic α- helices (Kaufmann et al., 2005). The first two helices are involved in dimerization, whereas the third helix in combination with the rest C-terminal domain may function in higher-order complex formation. The carboxyl (C) terminal domain can be very divergent. In yeast two-hybrid assays, GBD:MEA interacted with the AGL9 MADS domain from amino acid 1 to 60. Longer AGL9 sequences up to amino acid 172, which F&R Ref No.: 09531-0556WO1 includes the I and K domains, bound GBD:MEA equally well. However, the MADS domain, and the I and K domains were all required for AGL15 interaction with GBD:MEA. GBD:AGL9 barely interacted with full-length AGL15 or the MADS-box alone from amino acid 1 to 60. GBD:AGL9 strongly interacted with AGL15 MADS and I domains together from amino acid 1 to 84. When fused with GBD, AGL15 interacted with AGL9 truncation from amino acid 1 to 172 but not AGL9 full-length protein. Neither GBD:AGL9 or GBD:AGL15 formed homodimers in the yeast two-hybrid assays. In Nicotiana leaves, MEA:YFPNinteracted with either AGL9:YFPCor AGL15:YFPC. We then performed co-immunoprecipitation assays with transgenic plants that carry both MEA:MYC and AGL9:GFP or both MEA:MYC and AGL15:GFP. Anti-GFP antibodies effectively pull down MEA:MYC in plant protein extracts prepared from developing seeds at 4 to 5 DAP but no MEA:MYC was pulled down from the developing seeds at 4 to 5 DAP in the absence of anti-GFP antibodies. Example 23—The Expression of AGL9 and AGL15 Precedes the Repression of IKU2 and MINI3 Expression MEA was constitutively expressed from 1 to 7 DAP in developing seeds. However, by previous in situ hybridization analysis, MEA was expressed in free nuclear endosperm prior to cellularization at the periphery of the central cell (Vielle-Calzada et al., 1999). MEA transcript persisted at a high level in all cells of the suspensor and the embryo until the heart and torpedo stage. In a separate study, GUS activity driven by MEA promoter was found in dividing endosperm nuclei after fertilization (Luo et al., 2000). GUS activity was decreasing in the other nuclei before endosperm cellularization but was still strong in the chalazal cyst. We speculate that MEA protein may be stable and persist through the cellularization process. Indeed, MEA:MYC proteins were detected at a constant level at 2 to 3, 4 to 5, and 6 to 7 DAP in developing siliques from two independent transgenic lines. MEA:MYC protein detected at 4 to 5 DAP is probably derived from the endosperm as the embryo at the early heart to heart stage is tiny compared to the endosperm volume. MEA:MYC detected at 6 to 7 DAP are possibly produced in the embryo. In general, AGL9 has a relatively broad expression in leaf, cotyledon, stem, root, flower, embryo and seed (Pelaz et al., 2000; Favaro et al., 2002). In developing seeds, F&R Ref No.: 09531-0556WO1 AGL9 was expressed at a relatively low level from 1 to 3 DAP, and its expression reached a peak at 4 DAP and remained relatively high until 6 DAP. AGL15 is expressed during embryogenesis, but is also expressed in leaf primordia, shoot apical meristems and young floral buds (Rounsley et al., 1995). In developing seeds, the expression of AGL15 was barely detectable from 1 to 3 DAP, increased from 4 to 6 DAP, and returned to a low level at 7 DAP. Overall, the expression level of AGL15 was relatively low compared to that of AGL9. Similarly, AGL9:FLAG or AGL15:FLAG proteins accumulated at a low level at 2 to 3 DAP but their levels of accumulation were greatly increased after 4 to 5 DAP. To confirm the accumulation pattern of AGL9:FLAG or AGL15:FLAG, we examined the accumulation of AGL9:GFP and AGL15:GFP in developing siliques. Similar patterns of protein accumulation were observed for either AGL9:GFP or AGL15:GFP compared to those of AGL9:FLAG or AGL15:FLAG. A slightly higher level of GFP fusion proteins was observed at 2 to 3 DAP compared to that of FLAG-tagged proteins, and AGL9:GFP or AGL15:GFP might be slightly more stable. Control blots were probed with anti-tubulin 4 antibodies to ensure that we have an equal load of protein samples. Therefore, the expression and accumulation of AGL9 and AGL15 precede the repression of IKU2 and MINI3 expression by FIS-PRC2 at 4 DAP. However, AGL9 was reported to be expressed mostly in the early stage of seed coat and the expression in the endosperm was probably minimum (Belmonte et al., 2013; Picard et al., 2021). AGL15 was mostly expressed in the embryo. We examined the expression of AGL9:GFP and AGL15:GFP driven by their native promoters in the integument and the endosperm. Same laser power and exposure time were applied for imaging either the wild type control or the GFP-tagged seeds. Compared to the Ws control, AGL9:GFP signals were strong in the integument at 2 to 3 DAP but were not detected in the endosperm. AGL9:GFP signals at 4 to 5 DAP became much weaker in the integument compared to that at 2 to 3 DAP in the integument. In contrast, AGL9:GFP signals in the endosperm at 4 to 5 DAP became strongly visible. AGL15:GFP signals in the integument were visible at 2 DAP but became much weaker from 3 to 5 DAP in the integument. In the endosperm, AGL15:GFP signals were visible at 3 DAP and became strong at 4 to 5 DAP. We barely encountered Z-stacks with a single plane that shows a sound expression of either AGL9:GFP or AGL15:GFP in the embryo. In general, the embryo only occupies a small volume at 4 to 5 DAP. F&R Ref No.: 09531-0556WO1 Although the signals of AGL9:GFP or AGL15:GFP images were clearly present in the integument at 2 to 3 DAP, the relative amount of AGL9:GFP or AGL15:GFP proteins in total protein extracts prepared from siliques were probably low in protein blots. At 4 to 5 DAP, the levels of AGL9:GFP or AGL15:GFP proteins were high in the protein blots, representing increased expression and accumulation of the two fusion proteins in the endosperm plus the basal level of AGL9:GFP or AGL15:GFP accumulation in the integument. The accumulation of the AGL9:FLAG or AGL15:FLAG in protein blots showed a similar pattern to that of AGL9:GFP or AGL15:GFP proteins in protein blots. For example, AGL9:FLAG or AGL15:FLAG accumulation was low in total protein extract at 2 to 3 DAP, representing a basal level of the two fusion proteins. At 4 to 5 DAP, the high levels of AGL9:FLAG or AGL15:FLAG accumulation may represent the large amounts of AGL9:FLAG or AGL15:FLAG from the endosperm plus the relative low level of the two proteins in the total protein extracts from the integument. In summary, AGL9 and AGL15 expression precedes the suppression of IKU2 and MINI3 expression by FIS-PRC2; expression of MEA was not significantly different from each other from 1 to 7 DAP (by two-tailed Student’s t-test, p>0.05); expression of AGL9 was significantly different at various DAP (by two-tailed Student’s t-test, p<0.01); and expression of AGL15 was significantly different at various DAP (by two-tailed Student’s t-test, p<0.01 or p<0.05). Example 24—Mutations in AGL9 and AGL15 Enlarge Seed Cavity To investigate the biological function of AGL9 and AGL15 during seed development, we characterized 3 T-DNA insertion lines and created 4 Crispr knockout lines. For the AGL9 locus, a T-DNA was inserted in the first intron (SALK_136246) and the transcription of the AGL9 gene was disrupted in agl9-1. We created a clustered regularly interspaced short palindromic repeats (CRISPR) line with one of the CRISPR systems (Wang et al., 2015). A small deletion very close to the ATG codon of AGL9 was identified as agl9-2. Two T-DNA insertion lines were found for the AGL15 gene. One had a T-DNA insertion at the beginning of the second intron (SALK_093946) as agl15-2 and another had a T-DNA insertion in the 5thexon (SALK_076234) as agl15-3. agl15-2 was a knockout, but agl15-3 was a partial knockout since the transcript before the T-DNA insertion was still detected. agl9-1 and agl9-2 had a very similar but intermediate seed mass phenotype, with a F&R Ref No.: 09531-0556WO1 seed mass around 2.2 to 2.3 mg / 100 seeds (FIG.5A). Either the agl15-2 or the agl15-3 mutant did not exhibit any seed mass phenotype. We tried to cross T-DNA inserted agl9- 1 to either T-DNA inserted agl15-2 or agl15-3 and failed to identify double homozygous mutants that might cause lethality. We then intended to create double mutants by editing AGL9 in either agl15-2 or agl15-3 mutant background. We designed gRNAs against either the N-terminus or the C-terminus of AGL9. We failed to identify any homozygous lines for N-terminal AGL9 editing in either the agl15-2 allele or the agl15-3 allele background. We identified two C-terminal AGL9 editing lines in the agl15-2 background, one with a small deletion of 8 bp as agl9 agl15-2 c1, and another with a single nucleotide T insertion as agl9 agl15-2 c2. An additional line was identified with a small deletion of 47 bp in the C-terminal AGL9 in the agl15-3 background as agl9 agl15-3 c3. In each of the mutant alleles, a normal amount of mRNA was produced, but truncated protein might be made instead. All three agl9 agl15 double mutant alleles had significantly increased seed mass compared to the agl15-2 or agl15-3 single mutant (FIG.5B). Either agl9 agl15-2 c1 or c2 has a seed mass of around 3 mg / 100 seeds compared to that of agl15-2 with a seed mass of 1.83 mg / 100 seeds (FIG.5A and 5B). agl9 agl15-3 c3 had a seed mass of around 2.6 mg / 100 seeds.We also examined the expression of IKU2 and MINI3 in Col-0, agl9-1, and agl9 agl15-3 c3 developing seeds at 2 to 3 and 4 to 5 DAP. IKU2 and MINI3 expression was not affected at 2 to 3 DAP by either a single agl9 mutation or double agl9 agl15 mutations. At 4 to 5 DAP, single agl9-1 mutation elevated but double agl9 agl15-3 c3 mutations strongly elevated the expression of either IKU2 or MINI3. Shown in previous studies, overexpression of MINI3 has no influence on seed size and weight, but overexpression of IKU2 results in seeds with increased size and weight in Arabidopsis (Fatihi et al., 2013). Similarly, overexpression of MINI3 in Arabidopsis by our lab did not increase seed size (Xiao et al., 2016). Rather, overexpression of a canola IKU2 driven by MINI3 promoter in Arabidopsis delayed endosperm cellularization and increased the final seed mass of the transgenic lines. This would suggest that enlarged seeds in double agl9 agl15 mutants is likely due to higher expression of IKU2. Expression of AGL9:FLAG and AGL15:FLAG at 2 to 3 more times generated a small seed phenotype opposite to that of the agl9 agl15 double mutant (FIGs.5C). The expression of IKU2 and MINI3 in two AGL9:FLAG and two AGL15:FLAG transgenic lines was generally reduced at 2 to 3 DAP and especially at 4 to 5 DAP. We introduced AGL9:FLAG line #2 to agl9-1 and AGL15:FLAG line #14 to agl9 agl15 c1 by crossing. F&R Ref No.: 09531-0556WO1 Both lines have a transgene expression level close to that of wild type without an overexpression seed phenotype. AGL9:FLAG line #2 was able to rescue agl9-1 seed phenotype to wild type, whereas AGL15:FLAG line #14 was able to rescue agl9 agl15 c1 to a seed phenotype similar but slightly weaker than that of agl9-1. Expression of IKU2 and MINI3 was significantly different at 4 to 5 DAP (by two- tailed Student’s t-test, p<0.05 or p<0.01); expression of IKU2 was significantly different from that in Ws at 4 to 5 DAP and expression of MINI3 was significantly different from that in Ws at 2 to 3 DAP (by two-tailed Student’s t-test, p<0.05); enrichment of IKU2 probe 2 and MINI3 probes 3 or 4 with antibody at 4 to 5 DAP was significantly different from that of – antibody at 4 to 5 DAP (by two-tailed Student’s t-test, p<0.01); significant levels for the enrichment of IKU2 or MINI3 probes in the absence or presence of anti- H3K27me3 were p<0.05 or p<0.01 by two-tailed Student’s t-test; and significant level for enrichment of probes in the presence of anti-H3K27me3 antibodies between Col-0 and agl9 agl15-3 c3 by two-tailed Student’s t-test: IKU2 probes 2 and 3 or MINI3 probe 4 (p<0.01); IKU2 probe 4 or MINI3 probes 2 and 5 (p<0.05). We noticed a high level of silique abortion and seed abortion for the agl9 single mutant and the agl9 agl15 double mutant. Agl9-1 and agl9-2 showed a silique abortion rate of around 25%. The agl9 agl15-2 c1 and c2 mutants had a silique abortion rate of around 40%, whereas the agl9 agl15-2 c3 mutant showed a silique abortion rate of around 32%. Developing siliques from Col-0 and agl9 agl15-3 c3 plants were also dissected and examined for the rate of seed abortion from 2 to 6 DAP. Wild type Col-0 had a seed abortion rate of around 1 to 2%, whereas agl9 agl15-3 c3 siliques had an abortion rate of around 50%. Seed abortion occurred as early as 2 DAP in agl9 agl15-3 c3 siliques. Therefore, we examined seed abortion rates for all mutant genotypes at 5 to 6 DAP. Seed abortion rates were 30% for agl9-1 or agl9-2, 40 to 44% for agl9 agl15-2 c1 or c2, and 50% for agl9 agl15-3 c3. We next explored whether the abortion is due to insufficient delivery of pollen as the sepelata complex is responsible for the differentiation of stamen (Pelaz et al., 2000). The agl9 agl15 mutation might cause a reduction in pollen production. To distinguish between an early abortion of a fertilized seed or the phenotype of a non-fertilized ovule, we hand-pollinated the agl9 agl15 c3 mutant to ensure sufficient supply of pollen powders. Sufficient delivery of agl9 agl15 c3 pollens failed to rescue seed abortion phenotype, suggesting the involvement of a different mechanism. In addition, the mea F&R Ref No.: 09531-0556WO1 phenotype is female gametophytic and we performed reciprocal cross experiments to test the agl9 agl153c for maternal or paternal contribution over seed abortion and seed mass (FIG 6). Reciprocal cross experiments generated a very similar seed abortion rate, close to that of wild type. Similar results were also shown for the final seed mass (FIG.6). Thus, the function of AGL9 or AGL15 is zygotic or either AGL9 or AGL15 gene is not imprinted. In summary, silique abortion in Col-0 was significantly different from all single or double mutants (p<0.01 by two-tailed Student’s t-test) and the percentage of aborted seeds in Col-0 was significantly different from that in all mutant genotypes (p<0.01). Example 25—AGL9 and AGL15 are Required for the Targeting of FIS-PRC2 to the IKU2 and MINI3 Loci The ChIP association of MEA:YFPNwith the two loci was diminished in the agl9 agl15-2 c1 mutant siliques at 4 to 5 DAP. We also assessed the repressive H3K27me3 marks over three genomic regions of the IKU2 and MINI3 loci, two in the promoters and one in the coding sequences, in Col-0 and the agl9 agl15 mutant at 4 to 5 DAP. We sorted hexaploid endosperm nuclei using the ploidy-based FACS method after DAPI staining (Zheng and Gehring, 2019). The sorting profiles of nuclei isolated from developmental seeds showed six discrete peaks as 2C, 3C, 4C, 6C, 8C and 12C at 4 to 5 DAP. The ploidy peaks were compared with nuclei profiles obtained from leaf tissue, which is devoid of 3C and 6C nuclei. We harvested the sorted hexaploid endosperm nuclei with ConA beads and performed ChIP experiments with anti-H3K27me3 antibodies. The recovered ChIP DNA was used for qPCR analysis with primers against various regions in the IKU2 or MINI3 locus. H3K27me3 marks were enriched in regions cross the three probes in the IKU2 locus and the three probes in the MINI3 locus at 4 to 5 DAP in Col-0. However, the corresponding repressive marks were significantly reduced in agl9 agl15-3 c3 compared to that of Col-0 at 4 to 5 DAP. At 2 to 3 DAP, there were low level of the H3K27me3 marks around the probe 2 region at the IKU2 locus and the probe 4 region at the MINI3 locus in Col-0 but not in the agl9 agl15-3 c3 mutant. We also examined H3K27me3 marks in Ws, AGL9:FLAG line 11 and AGL15:FLAG line 4 at 2 to 3 and 4 to 5 DAP by ChIP-PCR. At 2 to 3 DAP, we detected a slightly enriched H3K27me3 marks for the probe 2 region at the IKU2 locus in Ws but not in the AGL9:FLAG or AGL15:FLAG overexpression lines. AGL9:FLAG or AGL15:FLAG overexpression significantly F&R Ref No.: 09531-0556WO1 enriched H3K27me3 marks at the coding region of the MINI3 locus at 2 to 3 DAP. At 4 to 5 DAP, most significant changes were noticed at the coding regions of both the IKU2 and the MINI3 loci in AGL9:FLAG or AGL15:FLAG overexpression lines. In summary, significant levels for the enrichment of IKU2 or MINI3 probes in the absence or presence of anti-H3K27me3 were p<0.05 or p<0.01 (by two-tailed Student’s t- test). Significant levels were shown between Ws and AGL9:FLAG and AGL15:FLAG transgenic seeds: p<0.05 or p<0.01 (by two-tailed Student’s t-test). There was no significant difference between AGL9:FLAG and AGL15:FLAG transgenic seeds from 2 to 9 DAP. Example 26—Mutations in AGL9 and AGL15 Knockouts Delay Endosperm Cellularization Compared to Col-0, either agl9-1 or agl9 agl15-3 c3 large seed cavity due to increased endosperm proliferation from 3 DAP at the globular stage until 9 DAP shown by differential interference contrast (DIC) images. No difference in embryo development was observed among Col-0, agl9-1 and agl9 agl15-33c mutants from 2 to 9 DAP. We presented quantitative data on DIC. The DIC analysis was stopped at 9 DAP since it becomes technically difficult to clear seeds. In general, the endosperm area is larger for agl9 and agl9 agl15 c3 mutants after 3 DAP compared to that of Col-0. The measurement was taken on a daily basis, and the difference may not be significant. In contrast, the seed mass was measured at the maturation stage as a result of accumulative development. Alternatively, the endosperm area may not well represent the three- dimensional volume of the developing endosperm. The number of nuclei is another way to indicate endosperm proliferation. However, the number of nuclei in early endosperm from 3 to 4 DAP was not significantly different between Col-0 and agl9-1 or agl9 agl15 c3. The agl9-1 and agl9 agl15 c3 mutants indeed had more endosperm nuclei at 5 DAP, but the numbers were not significantly different. To provide cellular resolution of the agl9 or agl9 agl15 developmental phenotype, we performed cellularization analysis for Col-0, agl9-1, and agl9 agl15-33c mutants from 2 to 6 DAP. Endosperm cellularization was followed by using a non-destructive method to generate green auto-inflorescence after treatment with 4% glutaraldehyde. Images were acquired with a confocal laser scanning microscope at an excitation wavelength of 488 nm (Liu et al., 2014; Xiao et al., 2016). Signals are usually strong in F&R Ref No.: 09531-0556WO1 the cell wall and the nucleus. We aimed to detect the presence of a cell wall. For image analysis, the progression edge of cellularization or the irregular border line was traced by Image J freehand selection close to reality rather than the specified points indicated. In Col-0, cellularization started from the micropylar endosperm, and several cellularized endosperm cells near the micropylar pole were obvious at 3 DAP or from the triangular to early-heart stage. Cellularization spread to the peripheral endosperm or nearly half of the central cavity at 4 DAP in Col-0. By 5 DAP, endosperm cellularization in Col-0 was completed. Cellularization was delayed in the agl9-1 mutant from 4 to 6 DAP and much delayed in the agl9 agl15-3 c3 mutant even at 6 DAP. The quantitative data on cellularization in Col-0, agl9-1 and agl9 agl15 c3 were also presented. The cellularized endosperm area was significantly less in the agl9-1 and agl9 agl15 c3 mutants compared to that in Col-0 from 3 to 6 DAP. At 4 and 5 DAP, the cellularization is much delayed in the agl9 agl15 c3 double mutant compared to that of agl9-1 single mutant. Overexpression of either AGL9:FLAG or AGL15:FLAG reduced endosperm cavity enlargement from 4 to 5 DAP through DIC analysis. The endosperm cavity was also smaller at 8 and 9 DAP in either the AGL9:FLAG or the AGL15:FLAG transgenic seeds. We performed cellularization analysis for the AGL9:FLAG and AGL15:FLAG transgenic seeds. Cellularization was much in the AGL9:FLAG transgenic seeds at 3 DAP but not in the AGL15:FLAG transgenic seeds (FIG.7). At 4 DAP, cellularization was significantly earlier for the AGL9:FLAG transgenic seeds (p<0.01) and less significantly earlier for the AGL15:FLAG transgenic seeds (p>0.05 but close to 0.05). There was no difference at 5 and 6 DAP for Ws and the AGL9:FLAG or the AGL15:FLAG transgenic seeds. Example 27—Global Targets of AGL9 and AGL15 with a Combined Change in H3K27me3 Marks and Gene Expression To identify genome-wide targets of MEA, AGL9 and AGL15, we examined the H3K27me3 repressive marks imposed by FIS-PRC2 in Col-0 and the agl9 agl15-3 c3 mutant at 4 to 5 DAP. We sorted hexaploid endosperm nuclei (Zheng and Gehring, 2019). We then performed low-input nCUT&Tag experiments with ConA beads and anti- H3K27me3 antibodies (Ouyang et al., 2021). The tagmented DNA was then PCR- amplified with i5 and i7 primers for 15 cycles. The PCR-amplified DNA was purified with AMPure XP beads and subject to high-throughput sequencing. Experiments were F&R Ref No.: 09531-0556WO1 performed with three biological replicates to facilitate statistical analysis and to cut down the number of false positives. The IgG control replicate 1 for agl9 agl15 c3 generated extremely low reads and was significantly deviated from the rest five IgG controls that were fairly consistent from replicate to replicate. We therefore used agl9 agl15 c3 IgG control replicate 2 to replace agl9 agl15 c3 IgG control replicate 1. Although the two controls were derived from different biological replicates, CUT&Tag experiments were performed side by side. We detected 1248 H3K27me3 peaks. The peaks were totally overlapped in Col-0 and the agl9 agl15 c3 mutant and no unique peaks were detected for either Col-0 or agl9 agl15 c3. The 1248 H3K27me3 peaks covered 8938 loci including IKU2 and MINI3. Comparing our CUT&Tag seq bedgraph file data with CUT&RUN seq bedgraph file data by Zheng and Gehring (2019), at least 90% overlap of the H3K27me3 peaks in 4 DAP endosperm was found. In contrast, our peak data has less overlap with INTACT ChIP-seq peak data, about 30-40% (Moreno-Romero et al., 2016). We presented the molecular and cellular analysis for the functional categories of the 8938 loci. The categories were enriched within the 8938 loci significantly (p<0.05) compared to the genome-wide categories of all Arabidopsis loci. Three categories are particularly interesting and include developmental processes in reproduction, nucleosome organization, and transcription factor activity. When the 8938 loci with H3K27me3 were compared between Col-0 and agl9 agl15-3 c3, 285 loci had reduced H3K27me3 marks and 157 loci had enriched H3K27me3 marks in agl9 agl15 c3 with a minimum 1.4-fold change up to 50-fold and p<0.05. There are no loci that completely lack H3K27me3 in the agl9 agl15 double mutant compared to wild type. One of the reasons is that we only looked at the seeds not aborted. Another reason is that we have partial loss-of-function mutants or weak agl9 agl15-3 alleles. True AGL9 and AGL15 double knockout cause lethality. Although AGL9 and AGL15 interact with MEA through their N-terminus, AGL9 and AGL15 C-terminus still have significant functions. For example, AGL9 C-terminal edit in agl15-2 or agl15-3 background generated a stronger seed phenotype compared to that of either agl15-2 or agl15-3 mutant without a visible seed phenotype (FIGs.5A and 5B). IKU2 and MINI3 loci did not meet the cut-off point but showed a clear tendency of reduced H3K27me3 marks. Through ChIP-qPCR analysis, the H3K27me3 marks were significantly reduced in agl9 agl15 c3 for both the IKU2 and the MINI3 loci. This discrepancy remains unclear to us. CUT&Tag was performed under in vivo condition and DNA maintains it native helix F&R Ref No.: 09531-0556WO1 turn, package and loop structure. The two loci might be relatively embedded in a highly packaged chromosomal area after trimethylation that makes it even less accessible to the anti- H3K27me3 antibodies in vivo. Both the IKU2 and the MINI3 loci indeed had much fewer read counts compared to their neighboring loci. Although the neighboring loci are nearby the MINI3 and IKU2 loci, and the various loci might be packed differently and may be in different helix turn or loop structure. In contrast, the H3K27me3 marks borne on sonicated DNA fragments would be readily accessible to anti-H3K27me3 antibodies by in vitro ChIP analysis. Target of AGL9 and AGL15 to a specific genomic region likely affects the expression of the corresponding gene at 4 to 5 DAP due to an enriched level of H3K27me3 marks. We next performed RNA-seq analysis in Col-0 and agl9 agl15-3 c3 developing seeds at 4 to 5 DAP and identified both up-regulated and down-regulated genes with a change at least two-fold and p<0.05. After assigning identities to these genes, we performed GO functional enrichment analysis to reveal the particularly enriched functions among the target genes. The GO terms with a similar function were further merged into two major categories: various biological processes and molecular and cellular functions. We categorized both up-regulated genes and down-regulated genes into various groups of molecular and cellular functions. The level of enrichment in a particular selected category was compared to the total Arabidopsis gene set and analyzed by Fisher's exact test. Shown in the large-scale RNA-seq data, the expression of IKU2 and MINI3 was increased by 1.62-fold and 3.94-fold, respectively, in the agl9 agl15 c3 double mutant, but the p value was >0.05. We performed qRT-PCR analysis on RNA isolated the same way as for large-scale RNA-seq. Both IKU2 and MINI3 were up-regulated in agl9 agl15 compared to that in Col-0. The 285 loci with reduced H3K27me3 marks and the 157 loci with increased H3K27me3 marks in the agl9 agl15-3 c3 mutant were further aligned with the up-regulated genes and down-regulated genes, respectively. Twenty-four loci were identified after aligning the 285 loci with up-regulated genes, whereas only 2 of the 157 loci were aligned with the down-regulated genes. It is probably due to minor contamination by 2C and 4C from the integument and the embryo. We piled up a short list of top 33 AGL9 and AGL15 targets from the 285 loci with reduced H3K27me3 marks. This short list also includes a few genes that were up- regulated (p<0.05) but did not meet the 2-fold cut-off point. Based on many in vivo and in vitro experiments, both IKU2 and MINI3 loci were enriched with H3K27me3 marks, and F&R Ref No.: 09531-0556WO1 both genes were up-regulated in the agl9 agl15 c3 double mutant. We added the IKU2 and MINI3 loci to this short list. We next carefully examined the expression of the remaining 252 loci with reduced H3K27me3 marks at least 1.4-fold and p<0.05. More than half of the 252 genes had extremely low levels of expression in Col-0, suggesting that the genes are suppressed at 4 to 5 DAP. Even with an up-regulation by the agl9 agl15 c3 mutations, reading bias against the low-abundant mRNAs could easily mask an up-regulation of the genes. Their expression changes could be explored by real-time qRT-PCR individually in the future. The rest of the 252 genes were grouped into three categories: an up-regulated expression above 2-fold but p>0.05, an up-regulated expression between 1 and 2-fold but p>0.05, and a slightly down-regulated expression but close to 1 and p>0.05. For some of the loci, changes in H3K27me3 marks may not be sufficient to impact gene expression. We performed gene cluster analysis and gene function annotations for potential AGL9 and AGL15 targets. To have a relatively large number of individuals for reliable and representative results, we focus on IKU2 and MINI3 plus the 285 loci that have at least 1.4-fold reduction of their H3K27me3 marks and a p value of less than 0.05. The functional enrichment analysis revealed particularly enriched functions among the selected genes. The terms with a similar function were further merged into two major categories: various biological processes and molecular and cellular functions. Among the various categories, eleven categories were particularly enriched compared to the whole genomic gene set, such as transcription, signal transduction, and reproduction. We then performed motif enrichment analysis for the 35 top AGL9 and AGL15 targets verified through CUT&Tag and expression analysis. One kb upstream regions of the 35 loci were used against 50 randomly shuffled genomic sequences. For the 35 targets, 198 hits were found for MADS box binding MIKC proteins. Only 56 hits were found for the shuffled genomic sequences. Example 28—AGL9, AGL15 and MEA Occupy the Six Representative Genomic Loci We selected six representative loci from the merger list. TCP15 (At1G69690) is a protein similar to TFL1 and regulates endoreduplication and the vegetative to reproductive phase transition (Ding et al., 2022). At2G35940 encodes BLH1 (BEL1- LIKE HOMEODOMAIN 1) or EDA29 (EMBRYO SAC DEVELOPMENT ARREST 29). Ecotopic expression of BLH1 in the embryo sac causes defects in nuclear migration and cellularization and embryo sacs with multiple egg cells (Pagnussat et al., 2007). F&R Ref No.: 09531-0556WO1 At2G42730 is a F-box protein and potentially regulates protein accumulation. At5G43270 encodes SPL2 or SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2. SPL10 and SPL11, SPL2 redundantly functions with SPL10 and SPL11 to control development of lateral organs in association with shoot maturation in the reproductive phase (Shikata et al., 2009). At5G55080 RAN4 is a member of the RAN GTPase family. At5G65310 encodes HOMEOBOX PROTEIN 5 that positively regulates ABA-responsiveness by mediating the inhibitory effect of ABA on growth during seedling establishment (Johannesson et al., 2003). The distribution of the H3K27me3 repressive marks upstream of the start codons to the 3’ UTR of six selected loci was shown by a normalized version of the genome browser view in Col-0 and agl9 agl15-3 c3.The H3K27me3 marks were densely deposited upstream of the transcription start site (TSS) to their exons for At1G69690 At2G35940, At2G42730 and At2G43270 at 4 to 5 DAP in Col-0. In contrast, the H3K27me3 marks were only deposited across the gene coding regions for At5G55080 and At5G65310. For all six loci, the H3K27me3 marks were significantly reduced due to the agl9 agl15-3 c3 mutations. To examine whether AGL9, AGL15 or MEA directly associate with the six representative genomic loci, we performed nCUT&Tag experiments with 4 to 5 DAP developing siliques from pAGL9::AGL9:FLAG, pAGL15::AGL15:FLAG, or pMEA::MEA:YFPNtransgenic lines (Ouyang et al., 2021). The developing siliques were harvested and protein–DNA complexes were cross-linked with formaldehyde for 10 min at 4^C after liquid N2grinding and the addition of a nuclei isolation buffer. The nuclei were then harvested by low-speed centrifugation for nCUT&Tag experiments with anti- FLAG or anti-GFP antibodies. In contrast to low-input CUT&Tag seq experiments for H3K27me3 marks, the nCUT&Tag experiments with pAGL9::AGL9:FLAG, pAGL15::AGL15:FLAG, or pMEA::MEA:YFPNtransgenic lines for high-throughput sequencing were not successful. A likely reason is that the limited genome binding sites of AGL9, AGL15, or MEA prevent the recovery of sufficient DNA tagmented for high- throughput sequencing. However, attempts using the tagmented DNA for qPCR analysis were successful and revealed a high detection sensitivity. The tagmented DNA was PCR- amplified with i5 and i7 primers for 15 cycles. The PCR-amplified DNA was further purified with AMPure XP beads and used for qPCR analysis with a 5’ primer derived from the i5 adaptor and a locus-specific primer (Table 1). AGL9:FLAG, AGL15:FLAG and MEA:YFPNwere indeed associated with the six representative genomic loci. We also F&R Ref No.: 09531-0556WO1 verified their expression in Col-0 and the agl9 agl15 c3 double mutant through qRT-PCR analysis. Expression of each gene in Col-0 was significantly different from that of agl9 agl15-3 c3 mutant at 4 to 5 DAP (by two-tailed Student’s t-test, p<0.05 or p<0.01). An agl9-2 mutant was generated with a Crispr gRNA against its N-terminus. agl15-2 and agl15-3 mutants were generated using a T-DNA insertion (FIG.8). The agl9 c agl15-2 or agl9 c agl15-3 double mutants edited with a Crispr gRNA were crossed against double agl9 c agl15 c mutant with AGL15 CRISPR in agl9 c background. A portion of the AGL9 C-terminus was disrupted using AGL9 and AGL15 C-terminal gRNAs. To eliminate seed abortion, we crossed agl9 c agl15-3 to Col and identified AGL9 C-terminal edited individuals in Col. We further edited AGL15 with a gRNA close to its C-terminus. This double mutant had both AGL9 and AGL15 edited close to their C- terminal ends. This double mutant produced large but not aborted seeds. A working model suggests that the expression of IKU2, MINI3 and other key genes for endosperm proliferation is activated after fertilization with a likely deposition of H3K27ac marks. Their expression is repressed at 4 to 5 DAP with the deposition of H3K27me3 marks by FIS-PRC2 recruited by the two AGLs (T-bar). Example 29—Summary of Results Table 2 shows the results to date with Arabidopsis, and Table 3 shows the results to date and expected results with Camelina. Table 2. Genes Gene origin Overexpression Phenotype Knockout Phenotype ARR11 Arabido sis Arabido sis Lar e seed Arabido sis Small seed e Table 3. Genes Gene origin Overexpression Phenotype Crispr Phenotype F&R Ref No.: 09531-0556WO1 (ongoing) seed ARR11 / SHB1 Arabidopsis Camelina Larger N / A N / A ( r t th r d d d e? Example 30— Homologs of AGL9 and AGL15 in Camelina Camelina has three AGL9 homologs and three AGL15 homologs, and it is possible that one, two or three homologs could be knocked out using a single gRNA. Example 31—Sequences Arabidopsis ARR11 promoter (shown with dotted underlining; nts 1- 1619) and genomic coding sequence (SEQ ID NO:94) TTGTCAAGTCTCTACGGGCCACGTCCTTATCCATAAAAAAGCTTTGTGCATGACAAGCTGTGTAC CATTTTCCTTTATTCTTTTGTCTTTCTACTTATTTTCTTTCAATAGAATATAAAGGTCAAAACAT

[0002] F&R Ref No.: 09531-0556WO1 ATATAATCCACAATATTATCATGTCAATATCTTAAGAACAATTTGAAAAGCTAAATTATTGGAAG AATATGGGATTATGGAGCAGTGAGAGACGTCAACTTACAAATTGAGAGAGAAAAGAGTTTCAACA ACTTTTTtttggcagtgaacttagaccgaactaaattccttcttcaaaagtaatccacaaataaa ttaatattttatagcctcgttttcaaattaaaaacagagagaaatttggaaattccagtacgacg ggagataaaacctaacatacgccatggtgaccgttatctaaactacgccaaaatatttgaagtgt cgtcgtttcataataaaacgcaaacaaaaacccactcccactttctcctttccaaaaaaagaact ctcgccactttctctgctctttttctttctctctctctttcttgttttcgccggcgatcATGGAG AAAAGCGGCTTCTCTCCCGTCGGTCTAAGGGTTCTTGTCGTAGACGATGATCCAACTTGGCTCAA GATTCTCGAGAAAATGCTCAAGAAGTGTTCTTACGAAGGTCTCTTTCTTCTTCTTCTATCTTATG TTTTCCCCAACAGTTGGATTTACTAAAATATCTCCTTACTTTCCTATGTTGCAGTAACGACCTGT GGATTAGCTAGAGAGGCTTTGAGGTTGCTGAGGGAGCGTAAAGATGGATATGATATCGTGATCAG CGATGTGAACATGCCTGACATGGATGGTTTCAAGCTTCTTGAGCATGTTGGTCTTGAATTAGACC TCCCTGTAATAAGTGAGAAGAAAGATCTTGACTTGTTGTGTAATAAATGAAAAAGGTTATTGATT TTTGTGTGTTTTGCGTTGTAGTGATGTCGGTGGACGGCGAAACAAGCCGAGTGATGAAGGGAGTG CAACACGGAGCTTGTGATTACCTCTTGAAGCCGATAAGAATGAAGGAGTTAAAGATTATATGGCA ACATGTTCTGAGAAAGAAGCTTCAAGAAGTGAGAGATATCGAAGGCTGTGGATACGAAGGAGGAG CGGATTGGATCACTCGATACGATGAAGCACATTTTCTTGGAGGTGGTGAAGATGTTTCTTTTGGG AAAAAGAGAAAAGACTTTGACTTTGAGAAGAAGCTTCTTCAAGATGAGAGTGATCCATCATCTTC TTCTTCCAAGAAAGCTAGAGTTGTTTGGTCTTTTGAGCTTCATCATAAGTTTGTCAACGCCGTTA ACCAAATCGGATGCGATCACAGTAAGTACGTTGGCGACTTTGGTTTCTTATCATGTCCCCTTGCC TCCCTTTATTATCATGTCTTCATAGAGCCGTGAAATTTTTTCCGGTCTCTTGTTTGGCAGAAGCT GGTCCCAAGAAGATATTGGATCTCATGAATGTTCCATGGCTCACTAGAGAAAATGTTGCAAGCCA CCTTCAGGTAAAAACTTTACCTTGTCATCATCATTATTCAGAACAAGTGTTAGATTAAGCTTTTC GTCACTTTTTTTTTGTTCTGTTTTTGTAGAAATATAGACTTTACCTGAGCAGATTAGAGAAAGGA AAGGAGCTCAAGTGTTATTCAGGTGGCGTGAAGAATGCGGATTCATCTCCAAAAGATGTCGAAGT GAATTCAGGCTACCAAAGCCCTGGGAGGAGCAGCTATGTATTCTCTGGAGGAAATTCTCTGATCC AAAAAGCAACAGAGATTGATCCAAAGCCACTTGCTTCAGCTTCTTTGTCTGACCTCAACACCGAT GTGATCATGCCTCCGAAAACAAAAAAGACGCGTATAGGATTTGATCCTCCCATTTCCTCCTCTGC GTTTGACTCTCTGCTTCCTTGGAATGATGTTCCAGAGGTCCTTGAATCGAAGCCGGTTCTGTATG AGAATAGCTTTCTCCAGCAACAACCATTGCCAAGTCAAAGTTCCTATGTTGCAAATTCTGCACCA TCTCTCATGGAGGAGGAAATGAAGCCTCCTTATGAGACACCAGCAGGAGGCAGTAGTGTGAATGC AGATGAGTTTCTCATGCCACAAGACAAGATCCCTACTGTAACCCTTCAAGATTTGGATCCCTCTG CCATGAAGCTGCAGGAGTTCAACACAGAGGCGATTCTGAGAAGCTTGAACTGGGAACTTCCAGAA TCACATCATTCTGTTTCTTTAGACACTGACTTAGACTTGACTTGGCTTCAAGGCGAGCGTTTTCT TGCAAACACCGGACTCCAGTTTCAAGATTACAGTAGTAGCCCATCACTCCTATCTGAGCTCCCAG CCCACCTTAATTGGTATGGAAATGAGCGGCTGCCTGACCCTGACGAGTATTCCTTCATGGTAGAC CAAGGTTTATTCATATCTTAA Note: Small letters indicate the 5’ UTR (untranslated region). Double underlining indicates the ATG and stop codon. Intron sequences are not shown in small letters for ARR11 genomic coding sequence. The entire sequence was introduced into Camelina. Arabidopsis ARR11 polypeptide (SEQ ID NO:111) MEKSGFSPVGLRVLVVDDDPTWLKILEKMLKKCSYEVTTCGLAREALRLLRERKDGYDIVISDVN MPDMDGFKLLEHVGLELDLPVIMMSVDGETSRVMKGVQHGACDYLLKPIRMKELKIIWQHVLRKK LQEVRDIEGCGYEGGADWITRYDEAHFLGGGEDVSFGKKRKDFDFEKKLLQDESDPSSSSSKKAR VVWSFELHHKFVNAVNQIGCDHKAGPKKILDLMNVPWLTRENVASHLQKYRLYLSRLEKGKELKC YSGGVKNADSSPKDVEVNSGYQSPGRSSYVFSGGNSLIQKATEIDPKPLASASLSDLNTDVIMPP KTKKTRIGFDPPISSSAFDSLLPWNDVPEVLESKPVLYENSFLQQQPLPSQSSYVANSAPSLMEE EMKPPYETPAGGSSVNADEFLMPQDKIPTVTLQDLDPSAMKLQEFNTEAILRSLNWELPESHHSV SLDTDLDLTWLQGERFLANTGLQFQDYSSSPSLLSELPAHLNWYGNERLPDPDEYSFMVDQGLFI S Arabidopsis SHB1 promoter (shown with dotted underlining; nts 1- F&R Ref No.: 09531-0556WO1 1585) and genomic coding sequence (SEQ ID NO:95) GAGACGGGTTTGGTAAGACGTTATTTAATAACAATTGTAAACTATAAAATAAAAATAAATAGATT TAATTTGCAAACTTTTATATATACTAATTTAAAAAATAAGTTGTCCGCGGGTTAAAATCTAGTCA TGGTTATTTTAATTAGGTGAAATCAGCCTTGGATAATTTTAAAAACTAAAACCAATTGTTTGTAA GTACAACCGCGACGCCTTGGTCTCTGAGAATCACGACATTGTGGTCAACACTGTGACACGGCTCG AAGAAGGGCTCGAGACGGCGGCTTACGAGACTACGTTTTTAAAGGCCGGAGAAGCAGGTGGCGAC TTTGAGGTTACCTTTTTTAGAACCCTAGATCGAGAATTCAACAAGGTAAATAACTTTTACAGGCT GAAAGTGGAGACAGCTAGAACTGAGGCTCTGGCTCTGAACAAACAAATGGATGCTTTGATTGCTT TCAGACACAAAGTCATGGATCAGAATCAGAAGAACCCTTCTGTCTTTGATTCAGTTTCAGAAGAC ATCAATGGCTCAGCTTCTGAGGTTGGATCATCTTCAAAGTGTACAGAACACAGTAAGTGAGTTTC TCATGTTCTGTTTTGGTTTCAATTTTGGCCTGTGAAGACTGAAAAGTATGAATCTTTATTATGTT TTGGTTAATCAGATGTGGCGTTAGCTGATCTTATGAGGAACGAAGATACATCGAATGAGAGTATT CTTGAGCGCATCAGGATGAACAAAACTCGAGAAATAACTCCTCTGTCCGCAATTAAAACTATACT CAAGGTCCATAAGCAGGACGAGCTCAAATTCACAAGAGATAATCTCAAGGAAGTGGAAAAGCGAC TTCAGGTAGCGTTCATTGAGTTTTATCAGAAGCTTCGACATCTTAAAAACTACAGCTTCTTGAAC GCTTCCGCTGTTTCCAAGATCATGAAGAAGTATGATAAGGTACTTAATTTCTGTTGATAATTTTG ACAAGCTTTTACAGCATTTACTCTAGTTTAATATATATGCTCTACTCTTTAGATAGCCAAAAGAA ATGCTGCGAAACTGTATATGGAGATGGTCGATAAATCTTTCCTCAGTAGCTCCGAAGAAGTAAGT ATCCTTCTTCTATCTAGGAAAATCGAAACATGAAACTTTAGTTTGAAGCTTTAAACATGTGCAGG TTCATAAGTTGTTGCTAAAGGTTGAATCTATTTTCATTGAACATTTCTCCAATTCAAATCGGAGG GAAGGGATGAGCCATTTAAGACCAAAAATAAATAAAGAACGTCATCTTATAACGTTTTCCACCGG TATATATATCAACACTACAATAACCAATCTTTTGACATGTATTTTCAAGAGTAATTCATCATTTT GTTCTGTTTTTTGTTTTGTTTTAGGCTTCTTTTTCGGCTGTGGTATTTCTCTCATTGTAGCTCTG GGTTTGATCATCCATGCTCGTAATATCATGGGTACACCGGGACAAAGAACTTATATGGAAACAAT GTTCCCTCTTTACAGGTCAGTAAAACGACCAAATATAAACCAAACACACTATCTCTGTCTCTGTG TAATATTCTTGAGATATATACATTTCATTTGCAGGTTTTTTGGGTTTGTAGTTTTGCACATGGAC GTGTACGCTGCTAATATCTACTTCTGGAGGCGATACCGTGTGAATTACTCCTTCATCTTTGGATT CAAACAAGGCACTGAACTTGGTTATAGACATGTTCTACTTCTCAGCTTTGGTCTTGGTACACTTT CTTTATGTGCTGTCTTATTAAACCTTGACATGGAAATGGATGCTCAAACAAAAGATTACAGATTA GTCACCGAACTTATCCCCCTCTTTCTTCTCGTAGTAAGTTCCTTCTATCTCTCTCTATTTCTCAG TACATTTTACACAACTCAATCTTTGTTTTTAGTAAGACTCGTTTCTCTGCATATTGCAGTTAGTG F&R Ref No.: 09531-0556WO1 ATTATCATTGTTCTCTGCCCCTTTAACATTTTGTATCGGTCAAGCCGATTCTTCTTCCTCTCGGT TCTGTTCCGCTGCATTGCTGCACCATTTTACGCGGTACCAACAACATATCCTCCTCTCCATTCAT CTGAAGCATAAACAGAAATGTTAAGAAGAATGTCTTCCATTTTTGCAGGTGCATCTTCCGGACTT TTTCTTGGGAGATCAACTAACAAGCCAGGTTCGAGAAAATCTATACTCGATAAGATAGCTTCATA CTTATTTTGATCGATGATTTCTGATTTAAACAATCAATGCTAGGTTCAAGCACTGAGGAGTCTAG AGTTCTACATATGCTACTATGGTTTTGGAGATTTCAGATATAGACGACGAAACACCTGCACATCA AATATTGGATTCAGAACATTCTACTTCATCGTCGCCGTTATACCTTACTGGTTACGGTTTCTTCA GTGCATCCGAAGAATGGTGGAAGACAGAGATCTGAGTCATGGCTACAATGGCATCAAATACCTTT TGACCATCGTTGCTGCTTCTCTTAGAACAGCTTATACTCTAAACCGAGGAAGCAACTGGAATATC ACAGCTTGGGTTTTCTCAGGAGTTGCAACGTTTTACGGAACTTACTGGGACATTGTTCTTGACTG GGGATTGCTTCAAAGAGGATGTAAGAATAGTTTCTTGAGAGACAAGCTTCTTGTTCCTCACAAAA CCGTGTACTACGCTGCAATGGTGAGAGCAAACAGAAAACAGCAATAACCTCTGTTTTTGTTTTTT CTTTATACATATATGGTGAAGATTGTTGCTTCATGTACTTGGCAGGTCCTGAATGTTTTGTTGAG GTTAGTGTGGTTGCAAACAGTTTTGGATCTGAAATTCTCTTTCTTGCATAGAGAAACTATGGTCG CGCTTATGGCTTGCCTTGAGATCATACGCAGAGGTATCTGGAACTTCTTTAGGTAAGCTCCGAGA CTGAGAAGATGGTGTTTTCATGCATGAATCTACACAAAACTAATGAAATGTAATTGTTGATTAGG CTGGAGAATGAGCATTTGAACAACGTTGGGAGATACAGGGCGTTCAAAACTGTCCCGTTACCGTT CAACTACGAAGAAGATGGAGATCATCATAACAATTAG Note: Double underlining indicates the ATG and stop codons. Intron sequences are not shown in small letters for SHB1 genomic coding sequence. The entire sequence was introduced into Camelina. Arabidopsis SHB1 polypeptide (SEQ ID NO:112) MRFGKEFVSQMIPEWQEAYIDYAYLKTILQDIQASRNRSDSNNQSSTPSFARNLTRRYNRDALVS ENHDIVVNTVTRLEEGLETAAYETTFLKAGEAGGDFEVTFFRTLDREFNKVNNFYRLKVETARTE ALALNKQMDALIAFRHKVMDQNQKNPSVFDSVSEDINGSASEVGSSSKCTEHNVALADLMRNEDT SNESILERIRMNKTREITPLSAIKTILKVHKQDELKFTRDNLKEVEKRLQVAFIEFYQKLRHLKN YSFLNASAVSKIMKKYDKIAKRNAAKLYMEMVDKSFLSSSEEVHKLLLKVESIFIEHFSNSNRRE GMSHLRPKINKERHLITFSTGFFFGCGISLIVALGLIIHARNIMGTPGQRTYMETMFPLYRFFGF VVLHMDVYAANIYFWRRYRVNYSFIFGFKQGTELGYRHVLLLSFGLGTLSLCAVLLNLDMEMDAQ TKDYRLVTELIPLFLLVLVIIIVLCPFNILYRSSRFFFLSVLFRCIAAPFYAVHLPDFFLGDQLT SQVQALRSLEFYICYYGFGDFRYRRRNTCTSNIGFRTFYFIVAVIPYWLRFLQCIRRMVEDRDLS HGYNGIKYLLTIVAASLRTAYTLNRGSNWNITAWVFSGVATFYGTYWDIVLDWGLLQRGCKNSFL RDKLLVPHKTVYYAAMVLNVLLRLVWLQTVLDLKFSFLHRETMVALMACLEIIRRGIWNFFRLEN EHLNNVGRYRAFKTVPLPFNYEEDGDHHNN Arabidopsis AGL9 genomic coding sequence (SEQ ID NO:96) ATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGC AAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTG CTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatct acttttgtatatatattacttataacataaacattttatatacatattaagtaacacaaaaatgt cttgtatgtatgggtctctctgtgatgtgttgttgtgtcgtacgtacgtgttctatcatatcctt ttaaaagaagcaaagaggaaaaaaaatttgggataccccaaatctgtatcattttataacaagtt tgcttttttgatgttcttttgtgtttctctttgatttccatttttgtttttgattttttttctat ttctctttacatctatcaaagttttttttcttatattttattgcttatttgtttgtctacttaat tcacattatctgagagaagaacaatctatctgatatgaaattagggttaatttctcttgtgagta ctctttaattcacataagcttaaagtttccaccttttgattctgggggtcgtccaattcgatcaa atcactcaattttgttgtcagattgatataagttcatagggggatattgtttccacgacaatcca ttttagtaacccttaggggtttccaattttgggttttgaattgacgctaatgtcaaattcatcta aagtccgttggatatgtatacttggggatgggattcatccttttttctgggttctttagatcttc tcttaaaagactaacagattttgttgtaaaccctaggaaacagttaaaaatcccatttttaaaaa catgttttgaacttgatgagtaagattaatggaagaaatgatgtttttgtgtggtgtgaagCATG CTTCGGACACTGGAGAGGTACCAAAAGTGTAACTATGGAGCACCAGAACCCAATGTGCCTTCAAG F&R Ref No.: 09531-0556WO1 AGAGGCCTTAGCAGTTgtacccaattctcttctctttcttctaattaccttaattaattactctc aatttttactttgatttttagagtcaaatgattaatgttataatttgtcatatacttcagGAACT TAGTAGCCAGCAGGAGTATCTCAAGCTTAAGGAGCGTTATGACGCCTTACAGAGAACCCAAAGgt aaactaattagcttcttcagctaccttcagagagtgtttgtttttttagtagatttttttgatgg ttttgatgttgaaatagGAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGA GTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGGgtactactttgtt catcaatatctttatacactgatctatttccatagtaagattaaatttggtgtttaattctgcag ACACAGTTTATGCTTGACCAGCTCAACGATCTTCAGAGTAAGgtaaataaagaaacactcattct cctctctaaattcctcatctaaaagtaatgtaaccaagaaaacacaaatatttggagcagGAACG CATGCTGACTGAGACAAATAAAACTCTAAGACTAAGGgtaattaatatacattctcatatcacca aattaatgcatcactaaatttggttataatgtgtgtgtgtatatacatatgtgacagTTAGCTGA TGGGTATCAGATGCCACTCCAGCTGAACCCTAACCAAGAAGAGGTTGATCACTACGGTCGTCATC ATCATCAACAACAACAACACTCCCAAGCTTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCAG ATCGGgtaactttagactagtataaccaatttgatttgagttctattataagcttttcttaagaa agtatctcaaactactaaattttatggagcagGTATCAGGGGCAACAAGATGGAATGGGAGCAGG ACCAAGTGTGAATAATTACATGTTGGGTTGGTTACCTTATGACACCAACTCTATTTGA Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the N-terminal and C-terminal gRNA sequences. Arabidopsis AGL9 polypeptide (SEQ ID NO:113) MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCSSSSMLR TLERYQKCNYGAPEPNVPSREALAVELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSTKELES LERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRLADGYQMPLQLNPNQEEVDHY GRHHHQQQQHSQAFFQPLECEPILQIGYQGQQDGMGAGPSVNNYMLGWLPYDTNSI Arabidopsis AGL9 N-terminal editing in agl9-2 (SEQ ID NO:97) ATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGC ACATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTGCTCTCATCATCTTCTCAAATAGAGGAAA GCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatctacttttgtatatatattacttataacat aaacattttatatacatattaagtaacacaaaaatgtcttgtatgtatgggtctctctgtgatgt gttgttgtgtcgtacgtacgtgttctatcatatccttttaaaagaagcaaagaggaaaaaaaatt tgggataccccaaatctgtatcattttataacaagtttgcttttttgatgttcttttgtgtttct ctttgatttccatttttgtttttgattttttttctatttctctttacatctatcaaagttttttt tcttatattttattgcttatttgtttgtctacttaattcacattatctgagagaagaacaatcta tctgatatgaaattagggttaatttctcttgtgagtactctttaattcacataagcttaaagttt ccaccttttgattctgggggtcgtccaattcgatcaaatcactcaattttgttgtcagattgata taagttcatagggggatattgtttccacgacaatccattttagtaacccttaggggtttccaatt ttgggttttgaattgacgctaatgtcaaattcatctaaagtccgttggatatgtatacttgggga tgggattcatccttttttctgggttctttagatcttctcttaaaagactaacagattttgttgta aaccctaggaaacagttaaaaatcccatttttaaaaacatgttttgaacttgatgagtaagatta atggaagaaatgatgtttttgtgtggtgtgaagCATGCTTCGGACACTGGAGAGGTACCAAAAGT GTAACTATGGAGCACCAGAACCCAATGTGCCTTCAAGAGAGGCCTTAGCAGTTgtacccaattct cttctctttcttctaattaccttaattaattactctcaatttttactttgatttttagagtcaaa tgattaatgttataatttgtcatatacttcagGAACTTAGTAGCCAGCAGGAGTATCTCAAGCTT AAGGAGCGTTATGACGCCTTACAGAGAACCCAAAGgtaaactaattagcttcttcagctaccttc agagagtgtttgtttttttagtagatttttttgatggttttgatgttgaaatagGAATCTGTTGG GAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGAGTCACTTGAGAGACAGCTTGATTCTTCC TTGAAGCAGATCAGAGCTCTCAGGgtactactttgttcatcaatatctttatacactgatctatt tccatagtaagattaaatttggtgtttaattctgcagACACAGTTTATGCTTGACCAGCTCAACG ATCTTCAGAGTAAGgtaaataaagaaacactcattctcctctctaaattcctcatctaaaagtaa tgtaaccaagaaaacacaaatatttggagcagGAACGCATGCTGACTGAGACAAATAAAACTCTA AGACTAAGGgtaattaatatacattctcatatcaccaaattaatgcatcactaaatttggttata atgtgtgtgtgtatatacatatgtgacagTTAGCTGATGGGTATCAGATGCCACTCCAGCTGAAC F&R Ref No.: 09531-0556WO1 CCTAACCAAGAAGAGGTTGATCACTACGGTCGTCATCATCATCAACAACAACAACACTCCCAAGC TTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCAGATCGGgtaactttagactagtataacca atttgatttgagttctattataagcttttcttaagaaagtatctcaaactactaaattttatgga gcagGTATCAGGGGCAACAAGATGGAATGGGAGCAGGACCAAGTGTGAATAATTACATGTTGGGT TGGTTACCTTATGACACCAACTCTATTTGA Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the N-terminal and C-terminal gRNA sequences. Arabidopsis AGL9 C-terminal editing in agl9 agl15-2 c1(SEQ ID NO:98) ATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGC AAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTG CTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatct acttttgtatatatattacttataacataaacattttatatacatattaagtaacacaaaaatgt cttgtatgtatgggtctctctgtgatgtgttgttgtgtcgtacgtacgtgttctatcatatcctt ttaaaagaagcaaagaggaaaaaaaatttgggataccccaaatctgtatcattttataacaagtt tgcttttttgatgttcttttgtgtttctctttgatttccatttttgtttttgattttttttctat ttctctttacatctatcaaagttttttttcttatattttattgcttatttgtttgtctacttaat tcacattatctgagagaagaacaatctatctgatatgaaattagggttaatttctcttgtgagta ctctttaattcacataagcttaaagtttccaccttttgattctgggggtcgtccaattcgatcaa atcactcaattttgttgtcagattgatataagttcatagggggatattgtttccacgacaatcca ttttagtaacccttaggggtttccaattttgggttttgaattgacgctaatgtcaaattcatcta aagtccgttggatatgtatacttggggatgggattcatccttttttctgggttctttagatcttc tcttaaaagactaacagattttgttgtaaaccctaggaaacagttaaaaatcccatttttaaaaa catgttttgaacttgatgagtaagattaatggaagaaatgatgtttttgtgtggtgtgaagCATG CTTCGGACACTGGAGAGGTACCAAAAGTGTAACTATGGAGCACCAGAACCCAATGTGCCTTCAAG AGAGGCCTTAGCAGTTgtacccaattctcttctctttcttctaattaccttaattaattactctc aatttttactttgatttttagagtcaaatgattaatgttataatttgtcatatacttcagGAACT TAGTAGCCAGCAGGAGTATCTCAAGCTTAAGGAGCGTTATGACGCCTTACAGAGAACCCAAAGgt aaactaattagcttcttcagctaccttcagagagtgtttgtttttttagtagatttttttgatgg ttttgatgttgaaatagGAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGA GTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGGgtactactttgtt catcaatatctttatacactgatctatttccatagtaagattaaatttggtgtttaattctgcag ACACAGTTTATGCTTGACCAGCTCAACGATCTTCAGAGTAAGgtaaataaagaaacactcattct cctctctaaattcctcatctaaaagtaatgtaaccaagaaaacacaaatatttggagcagGAACG CATGCTGACTGAGACAAATAAAACTCTAAGACTAAGGgtaattaatatacattctcatatcacca aattaatgcatcactaaatttggttataatgtgtgtgtgtatatacatatgtgacagTTAGCTGA TGGGTATCAGATGCCACTCCAGCTGAACCCAAGAGGTTGATCACTACGGTCGTCATCATCATCAA CAACAACAACACTCCCAAGCTTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCAGATCGGgta actttagactagtataaccaatttgatttgagttctattataagcttttcttaagaaagtatctc aaactactaaattttatggagcagGTATCAGGGGCAACAAGATGGAATGGGAGCAGGACCAAGTG TGAATAATTACATGTTGGGTTGGTTACCTTATGACACCAACTCTATTTGA Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the N-terminal and C-terminal gRNA sequences. Arabidopsis AGL9 C-terminal editing in agl9 agl15-2 c2 (SEQ ID NO:99) ATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGC AAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTG CTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatct acttttgtatatatattacttataacataaacattttatatacatattaagtaacacaaaaatgt F&R Ref No.: 09531-0556WO1 cttgtatgtatgggtctctctgtgatgtgttgttgtgtcgtacgtacgtgttctatcatatcctt ttaaaagaagcaaagaggaaaaaaaatttgggataccccaaatctgtatcattttataacaagtt tgcttttttgatgttcttttgtgtttctctttgatttccatttttgtttttgattttttttctat ttctctttacatctatcaaagttttttttcttatattttattgcttatttgtttgtctacttaat tcacattatctgagagaagaacaatctatctgatatgaaattagggttaatttctcttgtgagta ctctttaattcacataagcttaaagtttccaccttttgattctgggggtcgtccaattcgatcaa atcactcaattttgttgtcagattgatataagttcatagggggatattgtttccacgacaatcca ttttagtaacccttaggggtttccaattttgggttttgaattgacgctaatgtcaaattcatcta aagtccgttggatatgtatacttggggatgggattcatccttttttctgggttctttagatcttc tcttaaaagactaacagattttgttgtaaaccctaggaaacagttaaaaatcccatttttaaaaa catgttttgaacttgatgagtaagattaatggaagaaatgatgtttttgtgtggtgtgaagCATG CTTCGGACACTGGAGAGGTACCAAAAGTGTAACTATGGAGCACCAGAACCCAATGTGCCTTCAAG AGAGGCCTTAGCAGTTgtacccaattctcttctctttcttctaattaccttaattaattactctc aatttttactttgatttttagagtcaaatgattaatgttataatttgtcatatacttcagGAACT TAGTAGCCAGCAGGAGTATCTCAAGCTTAAGGAGCGTTATGACGCCTTACAGAGAACCCAAAGgt aaactaattagcttcttcagctaccttcagagagtgtttgtttttttagtagatttttttgatgg ttttgatgttgaaatagGAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGA GTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGGgtactactttgtt catcaatatctttatacactgatctatttccatagtaagattaaatttggtgtttaattctgcag ACACAGTTTATGCTTGACCAGCTCAACGATCTTCAGAGTAAGgtaaataaagaaacactcattct cctctctaaattcctcatctaaaagtaatgtaaccaagaaaacacaaatatttggagcagGAACG CATGCTGACTGAGACAAATAAAACTCTAAGACTAAGGgtaattaatatacattctcatatcacca aattaatgcatcactaaatttggttataatgtgtgtgtgtatatacatatgtgacagTTAGCTGA TGGGTATCAGATGCCACTCCAGCTGAACCCTAACCTAAGAAGAGGTTGATCACTACGGTCGTCAT CATCATCAACAACAACAACACTCCCAAGCTTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCA GATCGGgtaactttagactagtataaccaatttgatttgagttctattataagcttttcttaaga aagtatctcaaactactaaattttatggagcagGTATCAGGGGCAACAAGATGGAATGGGAGCAG GACCAAGTGTGAATAATTACATGTTGGGTTGGTTACCTTATGACACCAACTCTATTTGA Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the N-terminal and C-terminal gRNA sequences. Arabidopsis AGL9 C-terminal editing in agl9 agl15-3 c3 (SEQ ID NO:100) ATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGC AAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTG CTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatct acttttgtatatatattacttataacataaacattttatatacatattaagtaacacaaaaatgt cttgtatgtatgggtctctctgtgatgtgttgttgtgtcgtacgtacgtgttctatcatatcctt ttaaaagaagcaaagaggaaaaaaaatttgggataccccaaatctgtatcattttataacaagtt tgcttttttgatgttcttttgtgtttctctttgatttccatttttgtttttgattttttttctat ttctctttacatctatcaaagttttttttcttatattttattgcttatttgtttgtctacttaat tcacattatctgagagaagaacaatctatctgatatgaaattagggttaatttctcttgtgagta ctctttaattcacataagcttaaagtttccaccttttgattctgggggtcgtccaattcgatcaa atcactcaattttgttgtcagattgatataagttcatagggggatattgtttccacgacaatcca ttttagtaacccttaggggtttccaattttgggttttgaattgacgctaatgtcaaattcatcta aagtccgttggatatgtatacttggggatgggattcatccttttttctgggttctttagatcttc tcttaaaagactaacagattttgttgtaaaccctaggaaacagttaaaaatcccatttttaaaaa catgttttgaacttgatgagtaagattaatggaagaaatgatgtttttgtgtggtgtgaagCATG CTTCGGACACTGGAGAGGTACCAAAAGTGTAACTATGGAGCACCAGAACCCAATGTGCCTTCAAG AGAGGCCTTAGCAGTTgtacccaattctcttctctttcttctaattaccttaattaattactctc aatttttactttgatttttagagtcaaatgattaatgttataatttgtcatatacttcagGAACT TAGTAGCCAGCAGGAGTATCTCAAGCTTAAGGAGCGTTATGACGCCTTACAGAGAACCCAAAGgt aaactaattagcttcttcagctaccttcagagagtgtttgtttttttagtagatttttttgatgg F&R Ref No.: 09531-0556WO1 ttttgatgttgaaatagGAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGA GTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGGgtactactttgtt catcaatatctttatacactgatctatttccatagtaagattaaatttggtgtttaattctgcag ACACAGTTTATGCTTGACCAGCTCAACGATCTTCAGAGTAAGgtaaataaagaaacactcattct cctctctaaattcctcatctaaaagtaatgtaaccaagaaaacacaaatatttggagcagGAACG CATGCTGACTGAGACAAATAAAACTCTAAGACTAAGGgtaattaatatacattctcatatcacca aattaatgcatcactaaatttggttataatgtgtgtgtgtatatacatatgtgacagTTAGGTTG ATCACTACGGTCGTCATCATCATCAACAACAACAACACTCCCAAGCTTTCTTCCAGCCTTTGGAA TGTGAACCCATTCTTCAGATCGGgtaactttagactagtataaccaatttgatttgagttctatt ataagcttttcttaagaaagtatctcaaactactaaattttatggagcagGTATCAGGGGCAACA AGATGGAATGGGAGCAGGACCAAGTGTGAATAATTACATGTTGGGTTGGTTACCTTATGACACCA ACTCTATTTGA Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the N-terminal and C-terminal gRNA sequences. Arabidopsis AGL15 genomic coding sequence (SEQ ID NO:101) ATGGGTCGTGGAAAAATCGAGATAAAGAGGATCGAGAATGCGAATAGCAGACAAGTCACTTTTTC CAAGAGGCGTTCTGGGTTACTTAAGAAAGCTCGTGAGCTCTCTGTTCTTTGTGATGCTGAAGTTG CTGTCATCGTCTTCTCTAAGTCTGGCAAGCTCTTCGAGTACTCCAGTACTGGgtaacacttattt ctttttgattcaattttgtttttgcatgtcttgtcttgttgtgattagaatcgatttcgggaact gtaattgatttttgtttttgcatgtttgttaagattaaaagttttctgattgagctgaagagagt cctaattttgaattctcatttgattttagAATGAAGCAAACACTTTCCAGATACGGTAATCACCA GAGTTCTTCAGCTTCTAAAGCAGAGgtgagaatcattcattcttgtctcatatatcttgaaattg tttttttgaaaatctgattgctgtttagaacctccagGAGGATTGTGCAGAGGTGGATATTTTAA AGGATCAACTTTCAAAGCTTCAAGAGAAACATTTgtatggaaactaaataaatctcactatgctt gttcattactttattcttctctactttgtgtttgtttttagtgtttggctttgtgtgttctgttc tgttgtagACAACTGCAGGGCAAGGGCTTGAATCCTCTGACCTTTAAAGAGCTGCAAAGCCTTGA GCAGCAACTATATCATGCATTGATTACTGTCAGAGAGCGAAAGgtaactagtaatatcactcttc catcatcatttctctttgcattgtcctgattatggttatctgatttcagGAACGATTGCTGACTA ACCAACTTGAAGAATCACGCCTCAAGgtaaacactagcttttcctctctagcttccaaatgtaag cttatgtgtaatcacatgattctgaaccttgttaaaaccagtggctatcctttgacaagctcatg ctctaactagctagtgtgcagtttatttgtcttaagactcctatataactaggtacagagtgcaa aagtataattcgtttcttgattagccatatatatactttgcagGAACAACGAGCAGAGTTGGAAA ACGAGACCTTGCGTAGACAGgttcttattatttttgttgaatcatctcctaatgaacgcttcttc ctctgacttgtaattacttgttgaaacagGTTCAAGAACTGAGGAGCTTTCTCCCGTCGTTCACC CACTATGTTCCATCCTACATCAAATGCTTTGCTATAGATCCAAAGAACGCTCTCATAAACCACGA CAGTAAATGCAGCCTCCAGAACACCGATTCAGACACAACTTTGCAATTAGGgtattgctctttta agtctatttgctgtcattggttgcattattggaaagctgatttaagataaatataagtctttttc ctcctctgttagttatgcatatgccttaacactcactaactggagttataaaattcttactactt gtgttttctccaagGTTGCCGGGAGAGGCACATGATAGAAGGACGAATGAAGGAGAAAGAGAGAG CCCGTCAAGCGATTCAGTGACAACAAACACGAGCAGCGAAACTGCAGAAAGAGGGGATCAGTCTA GTTTAGCAAATTCTCCACCTGAAGCCAAAAGACAAAGGTTCTCTGTTTAG Note: Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the C-terminal gRNA sequence. Arabidopsis AGL15 polypeptide (SEQ ID NO:114) MGRGKIEIKRIENANSRQVTFSKRRSGLLKKARELSVLCDAEVAVIVFSKSGKLFEYSSTGMKQT LSRYGNHQSSSASKAENLQEDCAEVDILKDQLSKLQEKHLQLQGKGLNPLTFKELQSLEQQLYHA LITVRERKERLLTNQLEESRLKEQRAELENETLRRQVQELRSFLPSFTHYVPSYIKCFAIDPKNA LINHDSKCSLQNTDSDTTLQLGLPGEAHDRRTNEGERESPSSDSVTTNTSSETAERGDQSSLANS PPEAKRQRFSV F&R Ref No.: 09531-0556WO1 Arabidopsis AGL15 C-terminal editing shown in Fig 32E (SEQ ID NO:102) ATGGGTCGTGGAAAAATCGAGATAAAGAGGATCGAGAATGCGAATAGCAGACAAGTCACTTTTTC CAAGAGGCGTTCTGGGTTACTTAAGAAAGCTCGTGAGCTCTCTGTTCTTTGTGATGCTGAAGTTG CTGTCATCGTCTTCTCTAAGTCTGGCAAGCTCTTCGAGTACTCCAGTACTGGgtaacacttattt ctttttgattcaattttgtttttgcatgtcttgtcttgttgtgattagaatcgatttcgggaact gtaattgatttttgtttttgcatgtttgttaagattaaaagttttctgattgagctgaagagagt cctaattttgaattctcatttgattttagAATGAAGCAAACACTTTCCAGATACGGTAATCACCA GAGTTCTTCAGCTTCTAAAGCAGAGgtgagaatcattcattcttgtctcatatatcttgaaattg tttttttgaaaatctgattgctgtttagaacctccagGAGGATTGTGCAGAGGTGGATATTTTAA AGGATCAACTTTCAAAGCTTCAAGAGAAACATTTgtatggaaactaaataaatctcactatgctt gttcattactttattcttctctactttgtgtttgtttttagtgtttggctttgtgtgttctgttc tgttgtagACAACTGCAGGGCAAGGGCTTGAATCCTCTGACCTTTAAAGAGCTGCAAAGCCTTGA GCAGCAACTATATCATGCATTGATTACTGTCAGAGAGCGAAAGgtaactagtaatatcactcttc catcatcatttctctttgcattgtcctgattatggttatctgatttcagGAACGATTGCTGACTA ACCAACTTGAAGAATCACGCCTCAAGgtaaacactagcttttcctctctagcttccaaatgtaag cttatgtgtaatcacatgattctgaaccttgttaaaaccagtggctatcctttgacaagctcatg ctctaactagctagtgtgcagtttatttgtcttaagactcctatataactaggtacagagtgcaa aagtataattcgtttcttgattagccatatatatactttgcagGAACAACGAGCAGAGTTGGAAA ACGAGACCTTGCGTAGACAGgttcttattatttttgttgaatcatctcctaatgaacgcttcttc ctctgacttgtaattacttgttgaaacagGTTCAAGAACTGAGGAGCTTTCTCCCGTCGTTCACC CACTATGTTCCATCCTACATCAAATGCTTTGCTATAGATCCAAAGAACGCTCTCATAAACCACGA CAGTAAATGCAGCCTCCAGATTCAGACACAACTTTGCAATTAGGgtattgctcttttaagtctat ttgctgtcattggttgcattattggaaagctgatttaagataaatataagtctttttcctcctct gttagttatgcatatgccttaacactcactaactggagttataaaattcttactacttgtgtttt ctccaagGTTGCCGGGAGAGGCACATGATAGAAGGACGAATGAAGGAGAAAGAGAGAGCCCGTCA AGCGATTCAGTGACAACAAACACGAGCAGCGAAACTGCAGAAAGAGGGGATCAGTCTAGTTTAGC AAATTCTCCACCTGAAGCCAAAAGACAAAGGTTCTCTGTTTAG Note: Double underlining indicates the ATG and stop codons. Dashed underlining indicates the position of C-terminal editing. Camelina AGL9 and AGL15 homologs There are three Arabidopsis AGL9 homologs: Csa03g030490 (CsaAGL9- 1), Csa14g034830 (CsaAGL9-2), and Csa17g035980 (CsaAGL9-3). Only CsaAGL9-1 and CsaAGL9-3 rescued the Arabidopsis agl9-2 phenotype. Csa03g030490 (CsaAGL9-1, two splice variants that may code for different proteins with different start codons (shown with double underlining)) (SEQ ID NO:103) AGCCATAATAATAATAATAATAATGGTTTTCATATGTTAGGGTTTATGTAGGATTTCCAGTTTTT TATAATTCGATGATNGGTTAAAAAAAAAAAAAAAAAAGCATTCAACTTTCTTTAATTTAAACTAT TGGACCAGAGGATCACATTTCTCTAAACTATGGATTTGAAAATGAGAAACCACTAGCTCGAGAGT GGAATTCAAAAAAAATATTGTCTCCATTACTAATAATGTATAAACATAAAAATCCACCAAATTGC TAGGTTTGAAAAGAACTAAAGCATGTATAGAGTAATTAACGATTTTTTTTCAATTTGCAATATTT GAATAAATCCTATGAGGGTTCCTTTGGTACACAATAATTGGAGGGTATATAAATATAGTTGAGGG CTGAGAGAGAGTATATAGAAAGAGAATATTTCAAGTCATGAAGCTGACATGTTAATGTACTTGGA GAGAAGTGTTGTGAGACTTGTACAAATGTATATGTACACTTTAAAAAGAAATATAACATAGAGAA CAAATATAAACAAAACAAAAAAAAGAGAGAGAGAAGCTCATATATATATATATAGAATTGCTTGC AAAGAAAGAGAGAGAGAGAGAGAGATATTTGGGTAGAGAGAAAGAAAAGAAAAGAGAGAGAGAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGGGAAGGGGGAGAGTAGAATTGAAG AGGATAGAGAACAAGATCAATAGGCAAGTGACGTTTGCAAAGAGAAGGAATGGTCTTTTGAAGAA AGCATACGAGCTTTCCGTTCTGTGTGATGCAGAGGTTGCTCTCATCATCTTCTCAAATAGAGGAA AGCTGTACGAGTTTTGCAGTAGTTCGAGGTATATAGATATATATATCTATCTACTTTTGTATGTA TTACATACATATGTTATAACCAACATAAACAAATAAAAAAGAAATGTGTGTTTATGTATGTGTAT F&R Ref No.: 09531-0556WO1 GGGTCTTTCTGATGTGTTGTGTCGTACGTGTTCTATCATCCTTTTTAAAGAAGCAAAGAGGAAAT TTTTTTTTTTGGGATACCCAAAATCTGTTTCATTTAAATTAAAAAAAAAAAAAAAGATTGCTTTT TTACATGTTTTTGTGTTTTCTGATGATTTCCACTTCTGTTTTCTTTCTATTTTTTTTCCTTACAT CAAAGTTTTAATTCTTCTATTGCAGAATCCCCTAAGCTTTATTTGTTTGTCTATCCTTAGAAATT AATTATATATATAGGGGCTACTAAATATTATTTTATCTGAGAAGCTAAGTGAGAACAACCATCGA TCTGATATGAAAATTAGGGTTAATTTCTCTGGTTAGTGATGAATTAAATTAATTATAGTGTTTCT CTTTTGATTTGTACGTGGTCGTCCAATTCGATCAAATCACTCAATTTTTTTAATGTCAGAAGTTC TTAAGGGCTTTCCAATTTTGGTCTGAAGTGATGCCAATGTCAAATTCATATCTCAAAGCTATCCA TTGGATTTTTTTTTATTTTTTTTTATCCATTGGATTTATGTACTTGTGATCATCCTTGAACTTGA TTTTGAATTTATAGCCAAATTAAGCTTATTGGGGTCTTGAATTTGTTAACTAATGAAATGAATTA TTGTTTTATACGTCTGTAGCAGCATGCTTCGGACTCTTGAGAGGTACCAAAAATGTAACTATGGA GCACCAGAGCCCAATGTGCCTTCAAGAGAGGCCTTAGCAGTTGTACCCCTTCCTCTTTCTTCTTT CTTCTAATCTTAATTATAAAATCACACTCATTTTCTACTTACTTACTTAATTGTTCGGTAGAGAT CCAATGGTTAATGTTGTTTTGATACACTGCAGGAGCTAAGTAGTCAACAAGAGTATCTCAAGCTT AAGGAGCGTTATGACGCCTTACAAAGAACCCAAAGGTAACAACTAATCATAATTAATCAACTCCT AATTAAGCTAGCTAGCTAGCTAGCTAGGTGTACAGTCAAACTTGAATGGTTTTTGAATCTTGAAA TTATAGGAATCTACTGGGAGAAGATCTTGGGCCTCTAAGTTCAAAGGAGCTTGAGTCACTCGAGA GACAGCTTGATTCTTCCTTGAAGCAGATCCGAGCTCTCCGGGTACTATACCTTGTTTATCAGTTT CTCATATATGATCTGTACACTAGTAGTAATTAAGATATGCTATGTTAAAATATAATTGGGTTTAA TTAATTCTGCAGACACAGTTTATGCTCGACCAGCTCAACGATCTTCAGAGTAAGGTAAATACTAA CTACTCACATTAGCTCCTCTTTAATTCCAAATCTAGTATATATAACCACAAAAAAAAAAAAAAAA ATCGCAGGAACGCATGCTGACTGAGACAAATAAAACTCTAAGACTAAGGGTAATTGAATATAATT ATACACGTACTCGTCATTAATTAATTTGGTTAATAATAATGGTTTGAAGTAACGAAGAAAGTACT GTGTGTATGTGGCAGTTAGCAGATGGTTATCAGATGCCACTCCAACTGAACCCTAACCCAGAAGA TCATCTTGATCCCTATGGTCGTCATCATCATCAACAACAACACTCTCAAGCTTTCTTCCAGCCTT TGGAATGTGAACCCATTCTTCAGATCGGGTAACTAATTAACTTTATAACCAATTCTTAATTTGGT CTCCTTTGATTATTTATATAAGCTAGGTAGCATCGATCTTAATTAAACCAAGATTAATTAATATG CATCGTAATGATTATGGATCGTAGGTATCAGGGGCAGCAAGATGGAATGGGAGCAGGACCAAGTG TGAATAATTACATGTTGGGTTGGTTACCTTATGATACCAACTCTATTTGAAACTTTCTTAATAAT GAATTGCTTTCTTCTTCTTTTTTTGACATTTGAAGATGATCATGTTTCTTCTGATTTTATTACCT CTTATCATGTTTTCGGTCTTGTGTGCATGTGTGTGTGTAATAATGTTTAATTATAAAGCCCTTCT ATAATTCAATAATTTTGTCATCAGTTTTGCTACCCATATGTTTTACCCATTACTCCTAGCTACAC TCTCTCACACATNTTTTTTTTTTTTTTTTTTTTTGAGTTTGTTTTTAAGTATGCTTCCTCCTGCT GCAGATTGTTTTAGATCATCAACTCCCATTTTATGTTATGCGATGCTTTGTAAGTTTGTATATAT TATTAGTCATTAGACCACCATTAAGTCATTAACCAAAAACAAGAAAAACTCACACTACCTACTAC CTAGCTAGTTGTTTTTTTAAAATATCTTGTTTATCACATAACGATGAACTCACTGTAGGCCCATC TAATATCATTTTGGGCCATCTTTATACTCTTGTATATGGCCTATGTAAGAAGACTCATACTTCAT GAACTCCTCAAAATTTCACTATACCAAAATCTAATTAGAAAAAAAAACAGAAGAAAATTTCTAAG ACTAGGCCTGGCTCATATATTGACTGGGTCCTATGCAAAATAATTTTAGGTTTGACTTTCTGGAC ACAAATGATATGATTAGTATTATTACCAATCCAATCCAATCCACAAAAATAATTTGATGTACAAT CAATAAATTCGAATGATAACTTGATGTCTAACTTGCATGTTGTTCAATGATTGATCTCATCTTGT AACTTAATAAATGTCTTCATTTTTCTTTGTAATTTAAAAAATAAAAGGATTAGTGAAGATAATAA TGAATTATTGAAATGTTAATCATCTATATATAACTTAATAATATCTTCACTCTAATTTCTAATTA GTCATTTCACAAATCCA Note: The sequence up to the stop codon was used for Arabidopsis agl9-2 rescue. The italicized sequences are introns; the bold sequences are coding sequences. Dashed underlining indicates gRNA sequence for ongoing editing. Camelina AGL9 (Csa03g030490) protein sequence agl9-2 (SEQ ID NO:115) MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCSSSSSML RTLERYQKCNYGAPEPNVPSREALAVELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSSKELE SLERQLDSSLKQIRALRTQFMLDQLNDLQSKLADGYQMPLQLNPNPEDHLDPYGRHHHQQQHSQA FFQPLECEPILQIGYQGQQDGMGAGPSVNNYMLGWLPYDTNSI F&R Ref No.: 09531-0556WO1 Csa14g034830 (CsaAGL9-2, two splice variants that may code for different proteins with different start codons (shown with double underlining)) (SEQ ID NO:104) GATCCTGCAGACTTGCTGAAAATGCTTTAACGATCAAGCGAGATAATCAAAAGATTCAGTGTGCA AATCAAAGAAACTAAAATGGTTTAAATATAACCAAACAGAATAATAATGCTATGTTTAGTTTTTC TAATTGAATCATACCTTTGTGTCCATCACCTACTTACCGGTCAAAATAAAGCAATTACGTCTGCA ACCATAAAGCATATACTAAGAGTTTTGGTCAGACATGATCTCTAACATCGGACGAACCCTAAGAT AACCAATATAAACCATCACTTATATTCAAAACTCTGTTTATTTTATCCATTTATGTTTATTTTCT TCTTCTATATATACTTTTTTTTTTCTGTGTGTGTAGTCGCGTCAAACTCTCTCACACCAAACTGG ATTTTATCAACATGGTTTGTTTTATAAAGTGGATCATACTATAAACATTAATATATTTATATTAA GACCATATATACAAATTGGAAAACAAAAAGTATGTAGAACTATATACAAATTGGAAAACGATCGG AAAAAAAAAACAGATCTAGCAGTAAGAGAGATGTAGATATTATGAATCTAGCAGTAAAGAAGAAT AAAAAAACATGAATGAATCACAAAAGACGGTGTTTTTACTTTACATTTTTCACCAATCACAAGGG GTAGTTCCGTAAGTTGGGAAATTCGTACGAGGCTTCACCTAGTTAAGGTTAGGTCACATGATTCC CTGAACTCGTTTATAAAAGCAACCAAAATAAATAAAAACAAAAAATCCAAAATTTTTAAAATGTA GAAGAAAAAAATCAGGTGGATTTATCAGACCCTACCATCCAGATGTCGACACGTGTCCGAACTCA TTCATTGCCCTACTCTTTTCTGTTTAGGGTTGCCATCACTCATCACCCAAAGCCGCATCTCCACC GTCCATTTTTAGCTCTCATTTTCAACATCACTACTCTTATGAATCATACGATTTAATTATAAATA TCTCTGTCTCTCTCAACATATTAAAACCATAATAATAATAATAATAATAATGGTTTTCATATGTT AGGGTTTATGTAGGATTTCCAGTTTTTTATAATTCGATGATCATCCTCCAGGTTAAAAAAAAAAA GCATTAAACTTTCTTTAATTTAAACTACTGGGCCAGAGGATCACATTACTCTAAACTATGGATTT GAAAATGAGAAACCACTAGCTCGATAGTGGAATTCAAAAAAAAATATTGTCTCCATTACTAATAA TGTATAAACATAAAAATGCACCAAATTGCTAGGTTTGAAAAGAACTAAAGCACGGATAGAGTAAT TAACATTTTTTTCAATTTGCAATATTTGAATAAATCCTATGAGGGTTCCTTTGGTACACAATAAT TGGAGGGTATATAAATATAGTTGAGGGCTGAGAGAGAGAGTATATAGAAAGAGAATATTTCAAGT CATGAAGCTGACATGTTAATGTACTTGGAGAGAAGTGTTGTGAGATTTGTACAAATCTATATGTA CACTTTAAAAAGAAATATAACATAGAGAACAAATATAAACAAAACAAAAAAGAGAGNGAGAGAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG AGAGAGAGAGAGAGAGAGAGAAAGAGAGATATTTGGGTAGAGAGAAAGAAAAGAAAAGAGAGAGA GAATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAACAAGATCAATAGGCAAGTGACGTTT GCAAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGCTTTCCGTTCTGTGTGATGCAGAGGT TGCTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGGTATATAT ATATCTATCTACTTTTGTATCTATTACATACATATGTTATAACCAACATAAACAAATAAAAAAAG AAATGTGTGTTTTATGTATGTGTATGGGTCTTTCTGATGTGTTATGTCGTACGTGTTCTATCATC CTTTTTAAAGAAGCAAAGAGGAATTTTTTTTTTGGGATACCCAAATCTGTTTCATTTAAATTAAA TTAAAAAAAAAGACTGCTTTTTTACATGTTTTTGTGTTTTCTGATGATTTCCACTTCTGTTTTCT TTCTATTTTTTTTTTCCTTACATCAAAGTTTTAATTCTTCTATTGCAGAATCCCCTAAGTTTTAT TTGTTTGTCTATCCTTAGAAATTAATTATATATATAGGGGCTACTTAATATTATTTTATATGAGA AGCTAAGTGAGAACAACCATCGATCTGATATGAAAATTAGGGTTAATTTATCTGGTTAGTGATGA TTTAAATTAATTATAGGGTTTCTCTCTTTTGATTTGTGGTCGTCCAATTCGATGAAATCACACAA TTTTTTTAATGTCAGAAGTTCTTAAGGTCTTTCCAATTTTGGTTTCAAGTGATGCCAATGTCAAA TTCATATCTCAAAGCTATCCATTGGATATATGTACTTGTGACTCATCTTTGAACTTTATTTTGAG ATTATAGCCAAATAAGCTTATTGGGGACTTAAAGTTGTTAACTAATGAACTGAATTGTTGTTTTG TGTCGTAGCAGCATGCTTCGGACTCTTGAGAGGTACCAAAAATGTAACTATGGAGCACCAGAGCC CAATGTGCCTTCAAGAGAGGCCTTAGCAGTTGTACCCCTTCTCTTTCTTCTTTCTCTTCTAATCT TAATTATAATCATACTCATTTTCGACTTACTTAATTGTTCGGTCGAGATCCAATGATTAATGTTG TTTTGATACACTGCAGGAGCTAAGTAGTCAACAAGAGTATCTCAAGCTTAAGGAGCGTTATGACG CCTTACAAAGAACCCAAAGGTAACAACTAATTATAATTAATCAACTCCTTTAAGCTAGCTAGCTA CTATATATGTACAGTCAAACTTGATGAGTTTTGAATCTTGAAATTATAGGAATCTACTGGGAGAA GATCTTGGGCCTCTAAGTTCAAAGGAGCTTGAGTCACTCGAGAGACAGCTTGATTCTTCCTTGAA GCAGATCCGAGCTCTCCGGGTACTATACCTTGTTTATCAGTTTCTCATATGATCTGTACACTAGT AATTAAGATATGCTATGTTAAAATATAATTGGGTTTAATTAATTCTGCAGACACAGTTTATGCTC GACCAGCTCAACGATCTTCAGAGTAAGGTAAATACTAATTACTCACATTAGCTCCTCATTAATTC F&R Ref No.: 09531-0556WO1 CAAATCTAGTATATATAACCAAAAAAAAAAATCGCAGGAACGCATGCTGACTGAGACAAATAAAA CTCTAAGACTAAGGGTAATTTAATATAATTATACACGTACTCGTCATTAATTAATTTGGTTAATA ATGGTTTCAAGTAACGAAGCAAGTACTACTGTGTGTATGTGGCAGTTAGCTGATGGGTATCAAAT GCCACTCCAACTGAACCCTAACCCAGAAGATCATGTTGATCTCTATGGTCGTCATCATCAACAAC AACAACAACAACAACAGCACTCTCAAGCTTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCAG ATCGGGTAATTGATCATTAACTTTATAACCAATTCTTAATTTGGTCTGCTTTGATTATTTATATA AGCTAGGTAGCATGGATCTTAATTAAACCAAGATTAATTAATATCGTAATGATTATGGATCGTAG GTATCAGGCGCAGCAAGATGGAATGGGAGCAGGACCAAGTGTGAATAATTACATGTTGGGTTGGT TACCTTATGATACCAACTCTATATGAATCTTTCTTAATAATTAATTGCTTTCTTCTTCTTTTTCT TTTTTTTTTTCTTTTTTTTGACATTTTAAGATGATCATGTTTCTTCTGATTTTATTACCTCTATC ATGTTTTCGGTCTTGTGTGCATGTGTGTGTAATAATGTTTAATTATAAGCCCTTTCTATAATTCA ATAATTTTGTCATCAGTTTTGCCCCCATTACTCCTAAACTCTCACACATAAATTTTTTTCTTTGT TTTGAGTTTGTTTTGAAGTATGCTTCCTCCTGCTCCAGATTCTTTTAGATCATCAACTCCCATTT TATGTTATGCGATGCTTTGTATATATAATTAACCACCATTAACCAGAAACAAGAAAAACTCACAC TATCTAGCTAGTTGTTTTTTCAAAAAAAAAAAATATCTTGTTTATCAGATAACGATGAACTCACT GTAGGCCCATCTAATATCATTTTGGGCCATCTTTGTACTTTTGTATATGGCCTATGTAAGAAGAC CTATATACTTCATGAAACCATCAAAATTTCACTATACCAAAATCAGGAAAATAAAGAAGAAAAAA TATATATATAGTTAGAAAAAAGAAGAAGAAAATTTCTAAGAGTAGGCCTGGCTCATATATTGACT GGGTCCTATCCAAAATAATTTTAAGTTTGACTTTCTGGACACAAATGATATGATTAGTATTATTA CCAATCCAATCCACAAAAATAATTTGATGTACAAATCAATAAATTCGAATGATAACTTGATGTCT AACTTGCATGTTGTTCAATGATTCATCATCTTGTAACTTGATCATAATAGTATCTTCAACTTGGA ATTGGCAAAAAGAAAGGATTAGTGAAGATAAATAATGAATTATTGAAATGTCAATCTCTATATAT ACCTTAATAAATATCTTCACTCTATAATTTCTAATTAGTCATATCACA Note: The sequence up to the stop codon was used for Arabidopsis agl9-2 rescue. The italicized sequences are introns; the bold sequences are coding sequences. Dashed underlining indicates gRNA sequence for ongoing editing. Camelina AGL9 (Csa14g034830) protein sequence (SEQ ID NO:116) MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCSSSSMLR TLERYQKCNYGAPEPNVPSREALAELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSSKELESL ERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRLADGYQMPLQLNPNPEDHVDLY GRHHQQQQQQQQHSQAFFQPLECEPILQIGYQAQQDGMGAGPSVNNYMLGWLPYDTNSI Csa17g035980 (CsaAGL9-3, two splice variants that may code for different proteins with different start codons (shown with double underlining)) (SEQ ID NO:105) GGAAAACAAAAAGTATGTAGAACTATATACAAATTGGAAAACGATCGGAAAAACAGATCTAGCAG TAAGTAAGAGAGATGTAGATATTATGAATCTAGCAGTAAAGAAGAATAAAAAACATGAATGAATC ACAAAAGAGGGTGTTTTTACTTTACATTTTTCACCAATCACAAGGGGTAGTTCCGTAAGTTGGGA AAATCGTACGAGGCTTCACCTAGTTAAGGTTAGGTCACATGATTCCCTGAACTCGTTTATAAAAG CAACCAAAATAAATAAAAACAAAAAAAATCCAAAATTTTTAAAATTTAGAAGAAAAAAATCAGGT GGATTTATCAGACCCTACCATCCAGATGTCGACACGTGTCCGGACTCATTCATTGCCCTACTCTT TTCTGTTTGGGGTTGCCATCACTCATCACCCGAAGCCGCATCTCCACCGTCCATTTTTAGCTCTC ATTTTCAACATCACTACTCTTTATGTATCATACGATTTAATTATAAATATCTCTGTCTCTCTCAA CATATTAAAACCATAATAATAATAATGGTTTTCATATGTTAGGGTTTATGTAGGATTTCCAGTTT TTTTTATAATTCGATGATCATCCTCCAGGTTAAAGAAAAAAAGCATTCAACTTTCTTTAATTTAA ACTATTGGGCCAGAGGATCACATTTCTCTAAACTATGGATTTGAAAATGAGAAACCACTAGCTTC GAGAGTGGAATTCAAAAAAAAAAAATTGTCTCCATTACTAATAATGTATAAACATAAAAATGCAT CAAATTGCTAGGTTTGAAAAGAACTAAAGCATGTATAGAGTAATTAACGATTTTTTTTCAATTTG CAATATTTGAATAAATCCTATGAGGGTTCATTTGGTACACAATAATTGGAGGGTATATATAAATA TAGTTGAGGGCTGAGAGAGAGAGTATATAGAAAGAGAATATTTCAAGTCATGAAGCTGACATGTT AATGTACTTGGAGAGAAGTGTTGTGAGATTTGTACAAATGTATATGTACACTTTAAAAAGTAATA TAACATAGAGAACAAATATAAACAAAACAAAAAAAAAAAGAGAGAGAGAGAGAGAGACTCATATA TATATATAGAATTGCTTGCAAAGAAAGAGAGAGAGAGAGAGATATTTGGGTAGAGAGAAAGAAAG F&R Ref No.: 09531-0556WO1 AAAATTAAAGAGAGAGAGAGAGAGAGAATGGGAAGAGGGAGAGTAGAATTGAAGAGGATAGAGAA CAAGATCAATAGGCAAGTGACGTTTGCAAAGAGAAGGAATGGTCTTTTGAAGAAAGCATACGAGC TTTCCGTTCTATGTGATGCAGAGGTTGCTCTCATCATCTTCTCAAATAGGGGAAAGCTGTACGAG TTTTGCAGTAGTTCGAGGTATATATATATATCTATCTACTTTTGTATCTATTACATACATATATG TTATATAACCAACATATAAACAAATAAAAAAGAAATGTGTGTTTTATGTATGTGTATGGGTCTTT CTGATGTGTTGTGTCGTACGTGTTCTATCATCCTTTTTAAAGAAGCAAAGAGGAATTTTTTTTTT TTGGGATACCCAAAATCTGTTTCATTTAAATTAAAAAAAAAAAAAAAGATTGCTTTTTTACATGT TTTTGTGTTTTCTGATGATTTCCACTTCTGTTTTCTTTCTTTTTTTTTTTTCCTTACATCAAAGT TTTAATTCTTCTATTGCAGAATCCCCTAAGCTTTATTTGTTTGTCTATCCTTAGAAATTAATTAT ATATAGGGGAGACTTAATATTATTTTATCTGAGAAGCTAAGTGAGAACAACCATCGATCTGATAT GAGAATTAGGGTTAATTTCTCTGGTTAGTGATGAATTAAACTAATTATAGGATTTCTCTTTTGAT TTGTGGTCGTCCAATTCGATCAAATCACGCAACTTTTTTATGTCAGAAGTTCTTAAGGGCTTTCC AATTTTTTGGTTTGAAGTGAATAGTGATGCCAATGTCAATTCATATCTAAAAGCTAACCATATAT CTTGTGATCCATCCTTGAATTGTTTGTTTTGTGTGGTAGTAGCATGCTTCGGACTCTTGAGAGGT ACCAAAAATGTAACTATGGAGCACCAGAGCCCAATGTGCCTTCAAGAGAGGCCTTAGCAGTTGTA CCCCATTCTCCTTTTTCTTTCTTCTAATATTAATTAATTAATTAATTTACTCTCATTTTCTACCT AGCTTTAGTTAAGTAATTGTTCGATATCAAAGATCCAATGATTAATGATGATTTGATGATACACT ACAGGAACTTAGTAGCCAGCAGGAGTATCTCAAGCTTAAGGAGCGTTATGACGCCTTACAAAGAA CCCAAAGGTAACTAATTATAATTAATCAACTCCTTAAGCTAGCTAGCTACTATATGTACAGACAA CTTGATGACTTTTTTGAATCTTGAAATTATAGGAATCTACTGGGAGAAGATCTTGGGCCTCTAAG TTCAAAGGAGCTTGAGTCACTCGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCCGAGCTCTCC GGGTACTATACTTTGTTTATCACTTTCTCATATGATCTGTACACTATCAATTAAGATATGCTATG TTAAAATATAATTGGGTTCAATTAATTCTGCAGACACAGTTTATGCTCGACCAGCTCAACGATCT TCAGAGTAAGGTAAATACTAATTACTCACTAATATCTAGCTCCTCTTTAATTCCAAATCTTAGTA TATAACCAAAAACAAAATCGCAGGAACGCATGCTGACTGAGACAAATAAAACTCTAAGACTAAGG GTAATTTAATTAATATAATAATACACGTACTCATCATTAATTAATTTGGTTAATGGTTTGAAGTA ACAAAGCAAGTGTGTGTGTACTTGGCAGTTAGCTGATGGGTATCAGATGCCACTTCAACTGAACC CTAACCCAGAAGATCATATTGATCCCTATGGTCGTCATCATCATCAACAACAACAACAACACTCC CAAGCTTTCTTCCAGCCTTTGGAATGTGAACCCATTCTTCAGATCGGGTAACTGGATTAACTTTA TTTATTATCTATCTCATAACCAATTCTTAATGTGGTCTCCTTTGATTATATAACTAGAGCTAGCA TATCGATCTTAATTAAACCAAAGATTAATTAATATCGTAATGATTATGGATCGTAGGTCGTATCA GGCGCAGCAAGATGGAATGGGAGCAGGACCAAGTGTGAATAATTACATGTTGGGTTGGTTACCTT ACGATACCAACTCTATTTGAAACTTTCTTAATAATTAATTGCTTTCTTCTTCTTTTTTTTTGTTT TTTTTTGTTTTGAGATTTTAAGATGATGATCATGTTTCTTCTGAGTTTATTACCTCTATCATGTT TTCGGTCCTATTGTGTGCATGTGTGTGTAATAATGTTTAATTATAAAGCCCTTCTATAATTCAAT AATTTTGTCATCAGTTTTGCTCCCCATATGTGTTTTTACCCATTACTCCTACACTCTCACACATA AATCTTTTTTTTTTGTTTTTGTTTTAAGTTTGTTATTAAGTATACTTCCTCCTGCTCCAGATTCT TTTAAGAGCATCAACTCCCATTTTATGTTACGCGATACTTGTATATATAATTAAACCACCATTAA CCAAAAACAAGAAAAACTCACACTACCTAGCTAGTTGTTTTTTTTTGGACGTTGTTTATCACATA ACAATGAACTCACTGTAGGCCCATTTAATATCATTTTGGGCCATCTTTATACTTTTGCATATGGC CTATCATACTTCATGAACTCATCAAAATTTCACTAAACCAAAAATCAGGAAAAAAAGAAAAGAAA AAAAAATAAAACTAATTTAAAAAATAAAATTTCTAAGACTAGGCCTGGCTCATATATTGACTGGG TCCTATCCAAAATAATTTTAAGTTTGACTTTCTGGACACAAAATGATATGATTAGTATTATTACC AATCCAATCCACAAAAATAATGTGATGTACACAATCAATAAATTTGAATGATAACTTCATGTCTA ACTTGCTGTTCAATGATTCATCATCTTGTAACTTGATAATAATAATAATAATAATAATAACAATA CTAATAATAATAATAATAATAATAATAATAATCTATATAATAATAACAATTTGAAAAAATGCGAT CAACAGTTGTGTTTTTTCAATCGTACCTTTTGGATATTTTATGAAAAGTCGTGAAGGACCATTAA AACGGT Note: The sequence up to the stop codon was used for Arabidopsis agl9-2 rescue. The italicized sequences are introns; the bold sequences are coding sequences. Dashed underlining indicates gRNA sequence for ongoing editing. F&R Ref No.: 09531-0556WO1 Camelina AGL9 (Csa17g035980) protein sequence (SEQ ID NO:117) MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCSSSSMLR TLERYQKCNYGAPEPNVPSREALAELSSQQEYLKLKERYDALQRTQRNLLGEDLGPLSSKELESL ERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRLADGYQMPLQLNPNPEDHIDPY GRHHHQQQQQHSQAFFQPLECEPILQIGSYQAQQDGMGAGPSVNNYMLGWLPYDTNSI There are three Arabidopsis AGL15 homologs: Csa08g005750 (CsaAGL15-1), Csa13g016510 (CsaAGL15-2), and Csa20g019200 (CsaAGL15-3, a pseudogene). Only CsaAGL15-1 and CsaAGL15-2 rescued Arabidopsis agl9 c agl15-3 phenotype shown in Fig 33. Csa08g005750 (CsaAGL15-1, two splice variants that may code for different proteins with different start codons (shown with double underlining)) (SEQ ID NO:106) ACTATTAACAGTTGATACCATTTATGTTAATCACCAAAACAATGATATATACTATAGTATTTAAC TTAGGAATTTATAAGTAGAAACTGTTTGTACATTGTTGCTCACATTAAAGAAAGAGAAATATACA TTTTAAGTAAACAATATACAGTATAAATTTAAAAGAGAGAAGAAGAAGAAGAAGAAGAAAAAGAG GAAAAAAAACAACTTTATTTTAGTAAGAAAAGGGAAAGTAGGACCCAGAAGAACTGGCAAAATCC TCCAAATGTGGCAAAAAGGTGTCATGCAAATACTGTACCCCTCAAAAATTGAAAGAAAGCAAAAA TAATAGAAAGAGAGAGAGAGAGAGAGCACGCAAAACAGAGTCCATGCAACACACAACATTCATTA GTGGTTTTTTTCTTTTTTTCTTTCTAAAAAAATTATATTCCATCCAAATTTAGTAAACTCGGTGT TCCCATTAATAGATTCCCCCAAAACCCCCATTTCGGAGACGAGGAAGGTAGAAAGATTGAACCTT TCTTCTTCTTCTTCTTCTGTGTATTAATTTAAGGTGCGATATTGATTCAAAAAAATTGGGGGAAA AAGAAAAGAGAAGAGATGGGTCGTGGTAAAATCGAGATAAAGAGGATCGAGAATGCCAACAGCAG GCAAGTTACTTTCTCCAAGAGGCGTGCTGGTTTGCTTAAGAAAGCTCATGAGCTCTCTGTTCTTT GTGATGCTGAGGTTGCTGTCATCGTCTTCTCCAAGTCTGGCAAGCTCTTTGAGTTCTCCAGTTCT GGGTATCTACTTTTCACACTCTTTTTTTTTTTTTGATTCGATTTTGTATTTGCATGTCTTGATTT GATGTAAAATCGATTTGGGGATGGGGTTTAGTCTTTCCCTTAGTCAAAAAAATTGAATCTTTGCA TGTTTGTTTTGATCATTTTGAGTGTTAAAAGTTGTTTTCTGATTGAGCTAAATTTGATTTTTTAG GATGAAGAAAACACTTTCGAGATACGGCAACTACCAGAGTTCTTCAGATTCTAAAGTTGAGGTGA TAATTTTTGTGTTCATCTGTTGAAAAATTGTTCTGTTTTCTTTTCTGTATCTTAATCTGATTGTT GCCCGTTTAGAATCTCCAGGAGGAGGATTGTGCAGAGGTGGACCTTTTAAAGGATGAAATTTCAA AGCTTCAAAAGAAACATTTGTATGGAATCTTAATCCCACTTTTACTTTTCTATTCTTCTCTACTT TATCTTAAAAATGTTGTTTGGCTTTGTGTGTTTTTGTAGACAACTTCAGGGTAAGGGCTTGAATA TTCTGAACTTCAAAGAGCTGCAAAACCTTGAGCAGCAACTACATCATGCCTTGTTATCTGTGAGA GAGCGAAAGGTTAGTAGTTGACAGTTAACTAGTAATATCACTCTGTGTCTCATAATTCAGTTCTC TTTGCATTTTCCTAATAAAAGGTTATGTGATTTCAGGAACGGTTGTTGGCTATCCAACTTGAAGA ATCTCGCCTCAAGGTAAACAACAACACTCGCTTTTCCTCTTTAGCTTCCAACTGTGTATAACCAA ATGCAGTAAGCTTATGTGATCACATGATTCTGAACCTTTGTTAAAACCAATGTTCCCTCTATAGT GGTTACGATATTCTTTGACAAGCTTATGCTCTAACTAGCTAGCTAGTGTGTGCATTATGTTTGAC TTAAGACTCCTAACTAGGTACAGAGTACAAAAGTATAATTCTTTTCTTGACCAGCCATATAATAA TTTACTTTGCAGGAACAACGAGCAGAGTTGGAAAACGAGACCTTACGTAGACAGGTCCTTAATTA TAGTTTTCGTTGAGTCACCTCCAGTCGTGAATGGTTCATTCTCTGACTTCTCTCTTGAAACAGGT TCAGGAACTCAGAAGCTTTCTCCCGTCGTTCACTCACTATGTTCCATCCTACATCAAATGCTTCG CCATAGATCCCAGGAACGCTGTCCTAAACCATGGATGCTTGGACGACAGTAACTGCAGCCTCCAG AAAACCAATTCAGACACAACTTTGCAATTAGGGTATTGCTCTTATAATTTTCTGTTCATTGGTTC CAATATAGGAAACTCATTTTAGATATATAGTTGTCTTACTCTAGTATGCATATGTCTTAACACTA ATGGAATTATAAATTCTTTACTACTATGTCATATCTCCAAGGTTGCCGGGAGATGCACATGCACA TGATAGAAGGAAGAATGAAGGAGACAGAGAGAGCCCATCAAGCGATTCGGTGACAACAAACACGA CCACAGCAACTGCAGACAGGATCAGTCTAGTTTAGCAAAAATTTCCACCTGAAAACAAAAGCCAA AGGTTCTCTCTGTTTAGTGAGGTAGAGAATGTTTCCTCTTTAGCAAGTATCACATTATTTAAAGT AAATTTAGAAGAGATAACTTGCAAAAAACAAGAGAAGATTAACTTGATCTCATCTGCCTTTTCTC CTAATCTAACTCTCTGTACTTTTTCTATTGATTATTTTTCTGTCTCGTCTCAAATTTGTTAATAT GACACAAAGGTTAATTAATTATCTCGAGTAAGTAGTAAACAAAATACAATTGGAAGAAGTGACAA F&R Ref No.: 09531-0556WO1 AGAAGTAGCTTATAGTATTATCTGTGATTCTAAGACACACTGGGAAACAAGATATTTTTGGTATA CAAAGCTCTCTGTTTCTTTTTTACTTCCATCAAAGTAACAAATTAACCAAGTTACCAAATAAGAA GATCTTGTAAAAATAAACTTGGGGCAATCCAGAACACACCCCTAAAGTGAATGTTGTCGGAATTT TTCTACTTCATTACAATCAAAATTCATTAAAAAGGCCCAATTAGACCAGAATGTCCAACTAAAAA GTTTATAAGAATTTTTATCAATATTCCCCGAAACTATCAGCGAAAGTTTCAATAAGGACCCCGTA TTTTTCAGTTA Note: The sequence up to the stop codon was used for Arabidopsis agl9 c agl15-3 rescue. The italicized sequences are introns; the bold sequences are coding sequences. Camelina AGL15 (Csa08g005750) protein sequence (SEQ ID NO:118) MGRGKIEIKRIENANSRQVTFSKRRAGLLKKAHELSVLCDAEVAVIVFSKSGKLFEFSSSGMKKT LSRYGNYQSSSDSKVENLQEEDCAEVDLLKDEISKLQKKHLQLQGKGLNILNFKELQNLEQQLHH ALLSVRERKERLLAIQLEESRLKEQRAELENETLRRQVQELRSFLPSFTHYVPSYIKCFAIDPRN AVLNHGCLDDSNCSLQKTNSDTTLQLGLPGDAHAHDRRKNEGDRESPSSDSVTTNTTTATADRIS LV Csa13g016510 (CsaAGL15-2, two splice variants that may code for different proteins with different start codons (shown with double underlining)) (SEQ ID NO:107) AAGGCATGTGTGAGTGTATTTGAACATGCATGTTATGTACTTTCTTGGTTCCCAGAGGTGAACAT TAGTATTTGAACTTGTTTAGGGTGTTTGAAAAGACATATCATTGGTTACTTTTTCGAGGCAATAA GACCAAGAGTAAGTCCGTATCCTTGAATCTAAATCTGCTAATCAACATGAACATGAGATTAGAAT TTCTCTTTGATTTCTAATGTTTCCGATAATAAAAAGATTCATTAACTACATATTTACTGAATTGA GTGTCAAAAAAAATTTGGTGTTTTAAACCAAACTATTAACAGTTGATACCATGATGTTAATCACC AAAACAATGCTATATAGTATATTACTGTATATACTACTAGTATTTTAACTTAGAAATTTAAAAGT TGAAACTGTTTGTACATTGTTGCCCACATTAAAGAATGAGAAATATACATTTTAAGTAAACAATA AATAAATTTAAAAGAGAGAAGAAGAAGAGAAAAAAACAATTTTAGTAAGAAAAGGGAAAGTAGGA CCCAAAAGAACTGGCAAAATCCTCCAAATGTGGCAAAAATGTGTCATGCAAATACTGTACCCCTC AAAAATTGAAAGAAAGCAAAATTAAAAGAGAGAGAGAGAGAGAGAGCACGCAAAACAGAGTCCAT GCAACACACAACATTCATTAGTGTTTTTTTTTTCTAAAAAAATTATATTCCATCCAAATTTAGTA AACTCGGTGTTCCCATTAATAGATTCCCCCAAAAACTCCCATTTTGGAGACGAGGAAGGTAGAAA GATCGAACCTTTCTTTTTCTTCTTCTGTGTATTAATTTAAGGTGCGATATTGATTCAAAAAAATT GGGGGAAAAGAAAAGAGAAGAGATGGGTCGTGGTAAAATCGAGATAAAGAGGATCGAGAATGCCA ACAGCAGGCAAGTTACTTTCTCCAAGAGGCGTGCTGGTTTGCTTAAGAAAGCTCATGAGCTCTCT GTTCTCTGTGATGCTGAGGTTGCTGTCATCGTCTTCTCCAAGTCTGGCAAGCTCTTTGAGTTCTC CAGTTCTGGGTATNNNNNNNNNTTTTTTTTTTTTTTTTTTTTTGATTTTGTATTTGCATGTCTTG ATTTTTATGTGAATCGATTTGGAAATTGGAGACGGGGTTTAGTGTTTCCCTCAGTGAAAAAAAAA ATTGAGTCTTTTTTGCATGTTTGTTTTGATCATTTTGAGCTGAAAGAGAGTCTCTCTAATTTGAT TTGATTTATTAGGATGAAGAAAACACTTTCGAGATACGGCAACTACCAGAGTTCCTCAGATTCTA AAGCAGAGGTGATAATTTTTGTGTTCATCTGTTGAAAAATTGTTCTGTTTTCTTTTATGTATCTT AATCTGATTGTTGCCCGTTTAGAACCTCCAGGAGGAGGATTGTAAAGAGGTGGACCTTTTAAAGG ATGAAATTTCAAAGCTTCAAAAGAAACATTTGTATGGAATCTTGATCCCACTATCACTTTTCTAT TCTTCTCTACTTTGTCTTTACAATATTGTTTGGCTTTGTGTGTTCTTTAGACAACTGCAGGGTAA GGGCTTGAATATTCTGAGCTTCAAAGAGCTGCAAAACCTTGAGCAGCAACTATATCATGCCTTGA TATCTGTCAGAGAGCGAAAGGTTAATATTTGACAGTTAACTAGTAATATCACTCTGTTCTCATTC AATTCTCTTTGCATTTTCCTAATCAAAAGGTTATCTGATTTCAGGAACGGTTGTTGGCTATCCAA CTTGAAGAATCTCGCCTCAAGGTAAACAACAACACTAGCTTTTCCTCTTTAGCTTCCAACTGTGT ATAACCAAATGTAAGCTTATGTGATCACATGATTCTAAACCTTTGTTAAAACCAATGTTACTTCT ATTGTGGCTATGATATCCTTTGACAAGATTATGCTCTAACTAGGTTGCATTATGTTTGTCTTTAA GACTTCTAACGAGGTGCAAAGTGCAAAAGTATTTTTCTTTTCTTGACCAGCCATAATTTTTACTT GCAGGAACAGCGAGCAGAGTTGGAAAACGAGACCTTACGAAGACAGGTTCTTATAATTTGTGTTG AATCATCTTCGGTTATATATGAAAGTTCTTCGTCTGACTTCTAATTATTTCTTGACACAGGTTCA AGAACTCAGAAGCTTTCTCCCGTCGTTCACTCACTATGTTCCATCCTACATCAAATGCTTCGCCA TAGATCCCAAGAACGCTGTCCTAAACCATGGTTTCTTTGACGACAGTAACTGCAGCCTCCAGAAG F&R Ref No.: 09531-0556WO1 ACTAATTCAGACACAACTCTGCAATTAGGGTATTTCTCTTATAATTTGCCGTCATTGGTTCCAAT ATAGGAAACTCATCTTACTCTAGTATGCATAATTGCATAGGCCTCAACACTATATTGAAATTATA AATTCTTACTACTTTTGTCATTTCTCCAAGGTTGCCGGGAGAGGCACATAATAGAAGGAAGAAAG AAGGAGACAGAGAGAGCCCGTCAAGCGATTCAGTGACAACAAACACGACCAGAGGTACTGCAGAC AGGATCAGTCTAGCTTAATTAGCAAAATTTCCACCTGAAAACAAAAGTCAAAGGTTTTCTCTGTT TAGTGAGGTAGAGAATGTTTCCTCTTTAGCAAGTATCACATTATTTAAAGTAAGTTTAGAAGAGA TACTTGCAAAAAAAACAAGAGAAGATTAACTTTATCTCATCTGCATTTTCTCCTAATCTAACTCT CTGTTCTTTTTCTACTGATTGTTTTTCGTCTCGTCTCAAATTTGTTAATATGGCACAAAGTTAAT TAATATTTCGAGTAAACAAAATACAATTGGAAGAACTAACAAAGAAATAGCTTTTAGTATTATTA TTTGTGATTCTAATACACACTGGAAAACAAGATATTTTGCTACACAAAGCTCTCTGTTCCATTTT TACTTCCATCAAAGTAACAAATTAACCAAGTTACCAATTCGTTTTATCATATTGACCAATAAGAA GATCTTGTAAAAATAAACTTGGGGCATCCAGATCACACCCCTAAAGTGAAGGTTGTAGGAATCTT TCTACTTCATTACAATCATAATTCATTAAAAAGGCCCAATTGGACCAGAGTGTCGAAATAAAAAG TTTTAAGAATTTTATCAATATGCCCCGAAAAGTTTCAATAAGGACCCCATATTTTTCACTTAATT ACAATCCGTCCCCAGAAAAATAAAAGCTCGAGAAGGGATTATTAATTAGACCGAGAAAACCCTAA CCCCTCTTTATCCCCGCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA Note: The sequence up to the stop codon was used for Arabidopsis agl9 c agl15-3 rescue. The italicized sequences are introns; the bold sequences are coding sequences. Camelina AGL15 (Csa13g016510) protein sequence (SEQ ID NO:119) MGRGKIEIKRIENANSRQVTFSKRRAGLLKKAHELSVLCDAEVAVIVFSKSGKLFEFSSSGMKKT LSRYGNYQSSSDSKAEEEDCKEVDLLKDEISKLQKKHLQLQGKGLNILSFKELQNLEQQLYHALI SVRERKERLLAIQLEESRLKRAELENETLRRQVQELRSFLPSFTHYVPSYIKCFAIDPKNAVLNH GFFDDSNCSLQKTNSDTTLQLGLPGEAHNRRKKEGDRESPSSDSVTTNTTRGTADRISLA Csa20g019200 (CsaAGL15-3, pseudogene) (SEQ ID NO:108) CCAACTATTAACAGTTGATACCATTTATGTTAATCACCAAAACAATGCTATATAAGTAGAAACTG TTTGTACATTGTTGCTCACATTAAAGAAAGAGAAATATACATTTTAAGTAAACTATTATATAATT CAAAAGAGAGAAGAAGAAGGAGAAGAAGAAAAAAACAAGTTTCATTTAGTAAGAAAAGGGAAAGT AGGACCCAGAAGAACTGGCAAAATCCTCCAAATGTGGCAAAAAGGAGTCATGCAAATACTGTACC CCCCTCTAAAATTGAAAGAAAGCAAAAATAAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA GAGAGAGAGAGAGAGAGAGAGAGCACGCAAAACAGAGTCCATGCAACACACAACATTCATTAGTG TTTTTCACTTTTTCTTTTTCTTTTTCTAAAAGAATTATATTCCATCCAAATTTAGTAAACTCGGT GTTCCCATTAATAGATTCCCCCAAAAACCCCCATTTTGGATACGGGGAAGGTAGAAAGATTGAAC CTTTCTTCTTCTGCTTCTGCTTCTGCGTATTAGGTGCGATATTCATTCAAAAAAATTGGGGGAAA AAGAAAAGAGAAGAGATGGGTCGTGGTAAAATCGAGATAAAGAGGATCGAGAATGCCAACAGCAG GCAAGTTACTTTCTCCAAGAGGCGTGCTGGTTTGCTTAAGAAAGCTCATGAGCTCTCTGTTCTCT GTGATGCTGAGGTTGCTGTCATCGTCTTCTCCAAGTCTGGCAAGCTCTTTGAGTTCTCCAGTTCT GGGTATTTTATTTACTTTTCACACTCTTTTTTTTTATTCGATTTTGTATTTGCATGTCTTGATTT GATGTGAAATCGATTTGGGTACGGGGTTTAGTGTTTTCTGATACGACCTCAAGAAGCTTAATAGG CCTTAATGGGCTTGATTATTTAGTTTATTGTTTAAGCCCAAAATACTTAGAAGTCTCTTTGTATT TAATCTCACTTCCATTCTCTGTAAAACATTATCGAAATTAATCAAAACAATGTCATCTTCTTCCT TCATCGTCTCTCTCCTTCTTCTTCCTTCTTCCCTCTGATTTATTCACCTCAACCTCTATTTCTTC TGCTTCTCATCTCAAATTCTGTTATCTCCTTGATAAGCTACTTCGGTACTTTCAATTGGTGCTTT ACATCGAGAGTTTAAAAAAAAAAAAAAACA Note: This is a pseudogene and we did not perform rescue experiment for Arabidopsis agl9 c agl15-3. The italicized sequences are introns; the bold sequences are coding sequences. It is to be understood that, while the methods and compositions of matter have been described herein in conjunction with a number of different aspects, the foregoing F&R Ref No.: 09531-0556WO1 description of the various aspects is intended to illustrate and not limit the scope of the methods and compositions of matter. Other aspects, advantages, and modifications are within the scope of the following claims. Disclosed are methods and compositions that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed methods and compositions. These and other materials are disclosed herein, and it is understood that combinations, subsets, interactions, groups, etc. of these methods and compositions are disclosed. That is, while specific reference to each various individual and collective combinations and permutations of these compositions and methods may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular composition of matter or a particular method is disclosed and discussed and a number of compositions or methods are discussed, each and every combination and permutation of the compositions and the methods are specifically contemplated unless specifically indicated to the contrary. Likewise, any subset or combination of these is also specifically contemplated and disclosed.

Claims

F&R Ref No.: 09531-0556WO1 WHAT IS CLAIMED IS:

1. A modified oilseed plant exhibiting increased seed size and seed yield relative to a corresponding non-modified oilseed plant, wherein the modified oilseed plant comprises an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide.

2. The modified oilseed plant of claim 1, wherein the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

113.

3. The modified oilseed plant of claim 1, wherein the modified oilseed plant comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:

111.

4. The modified oilseed plant of claim 3, wherein the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

111.

5. The modified oilseed plant of claim 1, wherein the modified oilseed plant further comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:

112.

6. The modified oilseed plant of claim 5, wherein the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

112.

7. The modified oilseed plant of claim 1, wherein the modified oilseed plant further comprises an endogenous nucleic acid encoding an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:114, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL15 polypeptide.

8. The modified oilseed plant of claim 7, wherein the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:114.F&R Ref No.: 09531-0556WO1 9. The modified oilseed plant of claim 1, wherein the oil seed plant is selected from Camelina, pennycress, canola or soybean.

10. A method of increasing seed size and seed yield in an oil seed plant, comprising: disrupting expression of a first endogenous nucleic acid molecule in cells from the oil seed plant, wherein, prior to disrupting, the first endogenous nucleic acid molecule encodes an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the oil seed plant expresses little to no AGL9 polypeptide.

11. The method of claim 10, wherein expression of the first endogenous nucleic acid molecule in the cells from the oil seed plant is disrupted using gene editing.

12. The method of claim 10, wherein the AGL9 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

113.

13. The method of claims 10, further comprising: introducing a first exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the first exogenous nucleic acid molecule encodes an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:

111.

14. The method of claim 13, wherein the ARR11 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

111.

15. The method of claim 10, further comprising: introducing a second exogenous nucleic acid molecule into the cells from the oil seed plant, wherein the second exogenous nucleic acid molecule encodes an SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:

112.

16. The method of claim 15, wherein the SHB1 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:112.F&R Ref No.: 09531-0556WO1 17. The method of claim 10, further comprising: disrupting expression of a second endogenous nucleic acid molecule in the cells from the oil seed plant, wherein, prior to disrupting, the second endogenous nucleic acid molecule encodes an AGL15 polypeptide having at least 95% sequence identity to SEQ ID NO:

114.

18. The method of claim 17, wherein the AGL15 polypeptide has at least 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO:

114.

19. The method of claim 10, wherein the oil seed plant is selected from Camelina, pennycress, canola or soybean.

20. The method of claim 10, wherein expression and / or activity of endogenous MINI3 and / or endogenous IKU2 is / are increased in the oil seed plant.

21. A method of increasing seed size and seed yield in an oil seed plant, comprising: a) providing a first modified oilseed plant, wherein the modified oilseed plant comprises an endogenous nucleic acid encoding an AGL9 polypeptide having at least 95% sequence identity to SEQ ID NO:113, wherein the endogenous nucleic acid is disrupted and expresses little to no AGL9 polypeptide; b) providing a second modified oilseed plant, wherein the second modified oilseed plant: i) comprises an exogenous nucleic acid encoding an ARR11 polypeptide having at least 95% sequence identity to SEQ ID NO:111, or ii) comprises an exogenous nucleic acid encoding a SHB1 polypeptide having at least 95% sequence identity to SEQ ID NO:112; and c) crossing the first modified plant with the second modified plant to produce progeny plants, wherein the progeny plants exhibit increased seed size and seed yield.

22. The method of claim 21, wherein the first and the second oilseed plants are selected from Camelina, pennycress, canola or soybean.

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