DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
The amendments received on 03/06/2026 have been entered. Claims 85-86, 88, 90-104, and 106 are pending.
Claims 97-104 remain withdrawn for being directed to a non-elected invention(s).
Claims 89 and 105 have been cancelled.
Claims 85, 90, 92-94, 96, and 106 have been amended.
Claims 85-86, 88, 90-96, and 106 are examined in this Office Action.
The text of those sections of Title 35, U.S. Code, not included in this action, can be found in a prior Office action.
Objections and Rejections that are Withdrawn
All objections to and rejections of claims 89 and 105 have been rendered moot by Applicant’s cancellation of the claims.
The rejection of claim 106 under 35 USC 112(b) Indefiniteness has been withdrawn in light of Applicant’s amendment to the claim.
Written Description
Claims 86, 92, and 96 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim. This is a modified rejection necessitated by the claim amendments.
The claims are broadly drawn to the soybean plant or plant part thereof of claim 85, wherein the soybean plant or plant part has an increased level of mRNA produced by the endogenous gene comprising the at least one non-natural mutation; wherein the soybean plant or plant part thereof comprising the at least one non-natural mutation exhibits a phenotype of improved or maintained yield traits and/or improved plant architecture as compared to a control soybean plant.
Applicant describes:
The endogenous GRF gene GLYMA_11g008500 (SEQ ID NO: 72) and its coding sequence (SEQ ID NO: 73) (Specification, page 73, Table 1).
A 10bp (GTTCAAGAAA) out-of-frame deletion in GLYMA_11g008500 (SEQ ID NO: 72) resulting in SEQ ID NO: 133 (Specification, page 102, Table 3).
SEQ ID NO: 109 is the region of the miR396 binding site in GLYMA_11g008500 (SEQ ID NO: 72) from 968-989bp, which encompasses the 10bp deletion in SEQ ID NO: 133 (Specification, page 10, line 27).
The modification of an endogenous soy GRF transcription factor to disrupt miRNA396 action and increase GRF mRNA levels (Specification, Example 1, page 100).
Soybean plant CE56546 with a 6bp in-frame deletion in the miR396 target site in locus GLYMA_012234400 (SEQ ID NO: 75) showed an increase in miRNA levels (Specification, Example 1, page 100, and Figure 1).
The expression of GLYMA_ 128014700 (SEQ ID NO: 78) of the allele C combination showed an upregulation in gene expression in a 16-38-fold range (Specification, Example 4, page 104, and Figure 2).
The CE56564 allele combination B and CE56564 allele combination C suggest that in- frame deletions of GLYMA_12g014700 result in an increase in the number of pods on branches and pods per plant at the R6 stage of growth. The CE56564 allele combination B 5 family showed an increase in seeds per plant (Specification, Example 3, page 104, lines 2-6; and Table 4, page 103).
Applicant does not describe:
Mutated GRF transcription factor gene SEQ ID NO: 133 increasing miRNA levels.
A soybean plant comprising SEQ ID NO: 133 exhibiting a phenotype of improved or maintained yield traits, improved plant architecture and/or improved or maintained defense traits as compared to a control soybean plant (traits specifically recited in claims 92 and 96).
In regard to claim 86, the instant Specification describes soybean plant CE56546 with a 6bp in-frame deletion in the miR396 target site in locus GLYMA_01g234400 (SEQ ID NO: 75) showed an increase in miRNA levels; however, the other GRFs (including elected sequence SEQ ID NO: 72) showed relatively low % edit and no increase in mRNA levels (Specification, Example 1, page 100, and Figure 1).
The instant Specification further describes that leaf samples from three E2 plants derived from CE56564 and containing the allele combination C (SEQ ID NO: 134) were collected to evaluate expression levels of all four GRF genes. The expression of GLYMA_ 12g014700 (SEQ ID NO: 78) of the allele C combination showed an upregulation in gene expression in a 16-38-fold range. The other GRFs assayed (including elected sequence SEQ ID NO: 72) showed relatively low % edit, and no increase in mRNA levels (Specification, Example 4, page 104, and Figure 2).
The instant Specification states that these results show that in-frame deletions within the miR396 target of soybean GRFs can increase mRNA levels (Specification: Example 1, page 100, lines 29-30; Example 4, page 104, lines 15-17). It is noted that the mutation introduced into elected sequence SEQ ID NO: 72 to produce elected sequence SEQ ID NO: 133 is an out-of-frame mutation. Applicant has not reduced to practice an in-frame mutation in elected sequence SEQ ID NO: 72 that increases the level of mRNA produced, as required by the claim.
In regard to claims 92 and 96, Example 3 (pages 103 and 104) of the instant Specification shows the yield trait evaluation of the E1 generation of selected soybean plants. Neither the CE56564 allele combination A (elected sequence SEQ ID NO: 133) nor the CE56564 allele combination C (elected sequence SEQ ID NO: 133) are represented in Table 4 showing the phenotypic characteristics of the selected E1 plants. Thus, there is not support in the instant Specification for elected mutated sequence SEQ ID NO: 133 exhibiting a phenotype of improved or maintained yield traits, improved plant architecture, and/or improved or maintained defense traits as compared to a control soybean plant, as required by the claims.
Given that the Applicant has not reduced to practice an in-frame mutation, or any mutation, in elected sequences SEQ ID NOs: 72 or 73 which increases the level of mRNA produced, or confers the functions required by claims 92 and 96, there is not an adequate description to support the breadth of the claims.
Response to Applicant’s Arguments
Applicant's arguments filed 03/06/2026 have been fully considered but they are not persuasive.
Applicant argues that one of ordinary skill in the art would appreciate that Applicant has shown that an in-frame deletion in and/or adjacent to a miRNA binding site in an endogenous gene encoding a GRF transcription factor as claimed can result in an increased level of mRNA produced by the endogenous gene and a phenotype of improved or maintained yield traits and/or improved plant architecture (Remarks, page 2).
The Examiner respectfully disagrees. Applicant is claiming a group of endogenous genes encoding GRF transcription factors which comprise at least 90% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 76, 78, 79, 81, 82, 84, 85, 87, 88, 90, 91, 93, or 94. Applicant has elected SEQ ID NOs: 72 (genomic DNA), 73 (CDS), 74 (encoded protein sequence), and 133 (mutated from SEQ ID NO: 72). The instant Specification details mutations introduced into SEQ ID NOs: 72, 75, 78, and 81 and the selected mutation’s effects on yield traits. Table 4 (page 103-104) displays the phenotypic characteristics of E1 plants CE56564 (allele combination A; SEQ ID NO: 72), E1 plants CE56564 (allele combination B; SEQ ID NO: 78), E1 plants CE56564 (allele combination C; SEQ ID NO: 78), and E1 plants CE56540 (allele combination A; SEQ ID NO: 72). It is noted that an extremely small population of plants was tested for each family, ranging from 1-7, with the highest number (7) being the control. Applicant has shown CE56564 (allele combination B; SEQ ID NO: 78) and CE56564 (allele combination C; SEQ ID NO: 78), with testing populations of 5 and 3 respectively, increased the number of pods on branches and the number of pods per plant. Additionally, CE56564 (allele combination B; SEQ ID NO: 78) showed an increase in seeds per plant. Both CE56564 (allele combination B; SEQ ID NO: 78) and CE56564 (allele combination C; SEQ ID NO: 78) comprise in-frame mutations in the miRNA396 binding site, whereas both CE56564 (allele combination A; SEQ ID NO: 72) and CE56540 (allele combination A; SEQ ID NO: 72) comprise out-of-frame mutations in the miRNA396 binding site.
Additionally, Examples 6 and 7 (pages 105-107) disclose in-frame deletions in two lines CE59504 and CE58275 (SEQ ID NOs: 90 and 93). Of the many edits listed in Table 5 (page 105), no significant differences from wild-type plants were detected in any yield traits.
Thus, the instant Specification does not support an in-frame deletion in the miRNA396 binding site leading to an improvement in yield traits in elected sequence SEQ ID NO: 72. The instant Specification does not support an in-frame deletion in the miRNA396 binding site leading to an improvement in yield traits in any other sequence besides SEQ ID NO: 78. Therefore, given that the Applicant has not reduced to practice an adequate number of species to be representative of all in-frame mutations in and/or adjacent to an miRNA396 binding site in all endogenous genes encoding a GRF transcription factor having at least 90% sequence identity to SEQ ID NOs: 72, 73, 76, 78, 79, 81, 82, 84, 85, 87, 88, 90, 91, 93, or 94, there is not an adequate description to support the breadth of the claims.
Claim Rejections - 35 USC § 103
Claims 85-86, 88, 90-96, and 106 remain rejected under 35 U.S.C. 103 as being unpatentable over FU (Fu et al., International Publication Number WO 2019/158911 A1, International Publication Date 22 August 2019; included on IDS dated 08/29/2022) in view of BAUM (Baum et al., International Publication Number WO 2012/149316 A2, International Publication Date 1 November 2012). This is a modified rejection necessitated by the claim amendments.
Claim 85 recites “[a] soybean plant or plant part thereof comprising at least one non-natural mutation in an endogenous gene encoding a Growth Regulating Factor (GRF) transcription factor,
wherein the endogenous gene encoding the GRF transcription factor comprises a sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 73, and
wherein the at least one non-natural mutation is an in-frame deletion in and/or adjacent to a miRNA396 binding site in the endogenous gene, the miR396 binding site having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO:109”.
FU teaches and claims a method comprising introducing at least one mutation into at least one nucleic acid encoding a GRF (i.e., at least one non-natural mutation in an endogenous gene encoding a Growth Regulating Factor (GRF) transcription factor) (Fu, claim 5); wherein the mutation is in a micro RNA (miRNA) binding site, preferably an miRNA396 binding site (i.e., in and/or adjacent to a miRNA396 binding site in the endogenous gene) (Fu, claim 7); wherein the plant is selected from rice, maize, wheat, barley, sorghum, potato, tomato, soybean and B. napus (i.e., a soybean plant or plant part thereof) (Fu, claim 25).
FU further teaches that the mutation in the endogenous gene can comprise at least one mutation in any one of the following sites: the coding region of the GRF gene, preferably exon 3; a micro-RNA (miRNA) binding site, preferably at the miR396 binding site (i.e., in and/or adjacent to a miRNA396 binding site in the endogenous gene); an intronic sequence, preferably intron 2 and/or intron 3; and/or at a splice site, in the 5’UTR, the 3’UTR, the termination signal, the splice acceptor site or the ribosome binding site (Fu, page 31, lines 20-29).
FU teaches the miR396 binding or recognition site comprises or consists of the following sequence or a variant thereof, as defined herein:
CCGTTCAAGAAAGCCTGTGGAA: SEQ ID NO: 45
The miR396 binding site (SEQ ID NO: 45) as taught by FU shares 100% sequence identity with instant sequence SEQ ID NO: 109 (instant miR396 binding site) (i.e., the miR396 binding site having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 109) (see alignment below).
FU SEQUENCE SEQ ID NO: 45 ALIGNED WITH INSTANT SEQUENCE SEQ ID NO: 109
Qy 1 CCGTTCAAGAAAGCCTGTGGAA 22
||||||||||||||||||||||
Db 1 CCGTTCAAGAAAGCCTGTGGAA 22
FU teaches that the mutation that is introduced into the endogenous GRF gene or promoter thereof to increase the biological activity and/or expression levels of the GRF gene or protein may be: a "nonsense mutation" or "STOP codon mutation", which is a change in the nucleic acid sequence that results in the introduction of a premature STOP codon and, thus, the termination of translation (resulting in a truncated protein); plant genes contain the translation stop codons "TGA" (UGA in RNA), "TAA" (UAA in RNA) and "TAG" (UAG in RNA); thus any nucleotide substitution, insertion, deletion which results in one of these codons to be in the mature mRNA being translated (in the reading frame) will terminate translation; an "insertion mutation" of one or more amino acids, due to one or more codons having been added in the coding sequence of the nucleic acid; a "deletion mutation" of one or more amino acids, due to one or more codons having been deleted in the coding sequence of the nucleic acid; a "frameshift mutation", resulting in the nucleic acid sequence being translated in a different frame downstream of the mutation. A frameshift mutation can have various causes, such as the insertion, deletion or duplication of one or more nucleotides (Fu, pages 30 and 31, lines 22-34 and 1-12, respectively).
FU does not explicitly teach the endogenous gene encoding the GRF transcription factor comprises a sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 73.
However, BAUM teaches that nematodes are a very large group of invertebrate animals; some nematodes are plant parasites and can feed on stems, buds, leaves, and in particular on roots. Cyst nematodes are known to infect tobacco, cereals, sugar beets, potato, rice, corn, soybeans and many other crops. The soybean cyst nematode (Heterodera glycines) infests every soybean-producing state in the U.S., with total soybean yield loss estimates approaching $1 billion per year (Baum, page 1, lines 15-25).
BAUM teaches and claims methods to alter the genetic composition of crop plants, particularly those that are susceptible to nematode infection, thereby improving tolerance to nematode infection and reducing the effects thereof in plants. Baum further teaches and claims that miR396 and growth regulating transcription factors (GRF) with miRNA396 binding sites are connected through a negative feedback loop (Baum, page 3, lines 12-21; claims 1, 3-4, 8-9).
BAUM further teaches that the activity of a plant GRF polypeptide or microRNA is reduced or eliminated by disrupting the gene encoding a plant GRF polypeptide or microRNA by any method known in the art. For example, the gene may be disrupted by mutagenizing plants using random or targeted mutagenesis, and selecting for plants that have increased nematode tolerance (Baum, page 50, lines 15-22).
BAUM teaches SEQ ID NO: 21, a Glycine max GmGRF9 gene, which shares 100% sequence identity with instant sequence SEQ ID NO: 73 (i.e., the endogenous gene encoding the GRF transcription factor comprises a sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 73) (see alignment below). Baum sequence SEQ ID NO: 21 further comprises a region having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO:109 (i.e., the miR396 binding site having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO:109) (see highlighted region in box in the alignment below).
Baum sequence SEQ ID NO: 21 aligned with instant sequence SEQ ID NO: 73
Qy 1 ATGAGTAAGTGGCCTTTCACAATATCTCAGTGGCAGGAACTGGAACATCAAGCTTTAATT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 90 ATGAGTAAGTGGCCTTTCACAATATCTCAGTGGCAGGAACTGGAACATCAAGCTTTAATT 149
Qy 61 TACAAATACATGGTGGCTGGTCTTCCTGTGCCTCCTGATCTAGTCATTCCCATTCAGAAC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 150 TACAAATACATGGTGGCTGGTCTTCCTGTGCCTCCTGATCTAGTCATTCCCATTCAGAAC 209
Qy 121 AGCTTCCACTCCATTTCCCAAACCTTCTTGCACCATCCCTCTACCACCATGAGTTATTGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 210 AGCTTCCACTCCATTTCCCAAACCTTCTTGCACCATCCCTCTACCACCATGAGTTATTGT 269
Qy 181 TCCTTCTATGGGAAGAAGGTGGACCCGGAGCCAGGACGATGCAGGAGGACTGATGGGAAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 270 TCCTTCTATGGGAAGAAGGTGGACCCGGAGCCAGGACGATGCAGGAGGACTGATGGGAAA 329
Qy 241 AAGTGGAGGTGCTCCAAGGAAGCCTACCCAGACTCCAAGTACTGTGAGCGACACATGCAC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 330 AAGTGGAGGTGCTCCAAGGAAGCCTACCCAGACTCCAAGTACTGTGAGCGACACATGCAC 389
Qy 301 CGTGGCCGCAACCGTTCAAGAAAGCCTGTGGAATCACAAACTATGACACAGTCATCATCC 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 390 CGTGGCCGCAACCGTTCAAGAAAGCCTGTGGAATCACAAACTATGACACAGTCATCATCC 449
Qy 361 AATGTGTCATCATTGACTGTAACTGCTGGCAGCAGCACCAGTGCAACTGGAAATTTCCAG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 450 AATGTGTCATCATTGACTGTAACTGCTGGCAGCAGCACCAGTGCAACTGGAAATTTCCAG 509
Qy 421 AACCTTTCCACCACAAATGCATATGGTAATCCCCAAGGGACTGCTTCTGGAACAGACCAA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 510 AACCTTTCCACCACAAATGCATATGGTAATCCCCAAGGGACTGCTTCTGGAACAGACCAA 569
Qy 481 ACCCACTATCACATGGATTCCATTCCCTATGGGATCCCAAGTAAAGAATACAGGTATTTT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 570 ACCCACTATCACATGGATTCCATTCCCTATGGGATCCCAAGTAAAGAATACAGGTATTTT 629
Qy 541 CAAGGATCTAAATCTGAGGAACATAGTTTCTTGTCCAAAACTTTAGGAAGCAACAGGGTT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 630 CAAGGATCTAAATCTGAGGAACATAGTTTCTTGTCCAAAACTTTAGGAAGCAACAGGGTT 689
Qy 601 CTACACATGGAGCCACAGATGGACAACACTTTGATGCCAACCGGTGGAGTTGCCTCATTC 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 690 CTACACATGGAGCCACAGATGGACAACACTTTGATGCCAACCGGTGGAGTTGCCTCATTC 749
Qy 661 TCTACATTGAGATCAAATAATAATTCCATGTTGCAGGGTGATTATCTGCAGCCTTCTTTC 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 750 TCTACATTGAGATCAAATAATAATTCCATGTTGCAGGGTGATTATCTGCAGCCTTCTTTC 809
Qy 721 TTATCTAGTGAATATGCCTCGGCAGAAACTGTGAAGCAAGAGGGTCAGTCCCTTCGACCG 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 810 TTATCTAGTGAATATGCCTCGGCAGAAACTGTGAAGCAAGAGGGTCAGTCCCTTCGACCG 869
Qy 781 TTCTTTGATGAATGGCCTAAAAGCAGGGACTCATGGTCTGGTCTGGAAGATGAGAGATCC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 870 TTCTTTGATGAATGGCCTAAAAGCAGGGACTCATGGTCTGGTCTGGAAGATGAGAGATCC 929
Qy 841 AATCACACTCAACTCTCAATATCCATTCCTATGTCATCGTCAAATTTCTCTGCAACTAGC 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 930 AATCACACTCAACTCTCAATATCCATTCCTATGTCATCGTCAAATTTCTCTGCAACTAGC 989
Qy 901 TCTCATTCCCCACATGGTGAGATTTAA 927
|||||||||||||||||||||||||||
Db 990 TCTCATTCCCCACATGGTGAGATTTAA 1016
Additionally, BAUM teaches that all GFR transcription factors useful for the invention, will have an miRNA396 sequence (CAAGUUCUUUCGNACACCUU) (SEQ ID NO:27), and binding site AAGGUGUNCGAAAGAACUUGC (SEQ ID NO:28) in common.
Baum sequence SEQ ID NO: 28 AAGGUGUNCGAAAGAACUUGC
|||||||||||||||||||||
Instant sequence SEQ ID NO: 109 AAGGTGTCCGAAAGAACTTGCCA
(reversed)
Based on the teachings of FU and BAUM, it would have been obvious to use the method of introducing a mutation in the miR396 binding site in an endogenous GRF gene in soybean as taught by FU, together with the GRF transcription factor gene as taught by BAUM, SEQ ID NO: 21 which shares 100% sequence identity with instant sequence SEQ ID NO: 73. Each of the miR396 binding sites as taught by FU and BAUM have a finite number of nucleotides in which to introduce an in-frame deletion mutation. One of ordinary skill in the art would have been motivated to use the method of introducing a mutation in the miR396 binding site in an endogenous GRF gene in soybean, thus increasing the expression or levels of a growth regulatory factor (GRF) in a soybean plant or plant part thereof, as taught by FU. By combining the teachings of FU and BAUM, one having ordinary skill in the art would have a high expectation of success in achieving the soybean plant of instant claim 1.
The use of introducing mutations in plant genes to increase expression is a technique that was routine in the art at the time the application was filed, as taught by the cited references and the state of the art in general.
In regard to claim 86, FU teaches and claims a method of producing a plant with increased nitrogen uptake and/or nitrogen assimilation and/or nitrogen use efficiency, the method comprising increasing the expression or levels of a growth regulatory factor (GRF) or increasing the activity of a growth regulatory factor (i.e., wherein the soybean plant or plant part has an increased level of mRNA produced by the endogenous gene comprising the at least one non-natural mutation) (Fu, page 2, lines 20-24; claim 29).
In regard to claim 88, the protein encoded by Baum sequence SEQ ID NO: 21 shares 100% sequence identity with instant sequence SEQ ID NO: 74 and encompasses instant sequence SEQ ID NO: 110 (i.e., wherein the miR396 binding site of the endogenous gene encodes a region of a GRF polypeptide having at least 90% sequence identity to SEQ ID NO:110) (see highlighted region in box in the alignment below).
Protein encoded by Baum sequence SEQ ID NO: 21 aligned with instant sequence SEQ ID NO: 74
Qy 1 MSKWPFTISQWQELEHQALIYKYMVAGLPVPPDLVIPIQNSFHSISQTFLHHPSTTMSYC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSKWPFTISQWQELEHQALIYKYMVAGLPVPPDLVIPIQNSFHSISQTFLHHPSTTMSYC 60
Qy 61 SFYGKKVDPEPGRCRRTDGKKWRCSKEAYPDSKYCERHMHRGRNRSRKPVESQTMTQSSS 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 SFYGKKVDPEPGRCRRTDGKKWRCSKEAYPDSKYCERHMHRGRNRSRKPVESQTMTQSSS 120
Qy 121 NVSSLTVTAGSSTSATGNFQNLSTTNAYGNPQGTASGTDQTHYHMDSIPYGIPSKEYRYF 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 NVSSLTVTAGSSTSATGNFQNLSTTNAYGNPQGTASGTDQTHYHMDSIPYGIPSKEYRYF 180
Qy 181 QGSKSEEHSFLSKTLGSNRVLHMEPQMDNTLMPTGGVASFSTLRSNNNSMLQGDYLQPSF 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 QGSKSEEHSFLSKTLGSNRVLHMEPQMDNTLMPTGGVASFSTLRSNNNSMLQGDYLQPSF 240
Qy 241 LSSEYASAETVKQEGQSLRPFFDEWPKSRDSWSGLEDERSNHTQLSISIPMSSSNFSATS 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LSSEYASAETVKQEGQSLRPFFDEWPKSRDSWSGLEDERSNHTQLSISIPMSSSNFSATS 300
Qy 301 SHSPHGEI 308
||||||||
Db 301 SHSPHGEI 308
In regard to claims 92 and 96, FU teaches and claims increasing grain yield in the plant; an increase in grain numbers per panicle or per plant and/or an increase in 1000-grain weight (i.e., wherein the soybean plant or plant part thereof comprising the at least one non-natural mutation exhibits a phenotype of improved or maintained yield traits, improved plant architecture and/or improved or maintained defense traits as compared to a control soybean plant) (Fu, page 2, lines 13-15; claims 3-4).
In regard to claim 94, FU teaches and claims a method comprising introducing at least one mutation into a least one nucleic acid encoding a GRF (i.e., a Growth Regulating Factor (GRF) transcription factor gene that comprises a mutation) (Fu, claim 5); wherein the mutation is in a micro RNA (miRNA) binding site, preferably a miRNA396 binding site (in the nucleotide sequence of SEQ ID NO:109; it is noted that instant sequence SEQ ID NO: 109 is an miR396 binding site) (Fu, claim 7); wherein the plant is selected from rice, maize, wheat, barley, sorghum, potato, tomato, soybean and B.napus (i.e., a soybean plant) (Fu, claim 25).
Baum teaches SEQ ID NO: 21, a Glycine max GmGRF9 gene, which shares 100% sequence identity with instant sequence SEQ ID NO: 73 (i.e., the GRF transcription factor gene comprises a sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 73) (see alignment above).
In regard to claims 90, 91, 93, 95, and 106, although neither Fu nor Baum explicitly teaches the specific mutations recited in the claims, absent unexpected results, these specific variants would be obvious. As stated in the instant Specification, “an additional aspect of the invention provides a soybean plant or part thereof comprising at least one non-natural mutation within a mR396 binding site sequence or adjacent to a miR396 binding site sequence of an endogenous GRF transcription factor gene, wherein the at least one non-natural mutation prevents or reduces binding of miR396 to an mRNA produced by the endogenous GRF transcription factor gene resulting in an increased level of the mRNA produced by the endogenous GRF transcription factor gene” (Specification, page 2, lines 26-31). Fu specifically points to introducing a mutation in the miR396 binding site, and further teaches “the mutation is any mutation that prevents the cleavage of the sequence by microRNA and thus its subsequent degradation. This results in an increase in the levels of both GRF mRNA and protein” (Fu, page 31, lines 31-34). Additionally, Baum teaches that “mutations in conserved residues are particularly effective in inhibiting the activity of the encoded protein. Conserved residues of plant GRF polypeptides and/or miRNA396 suitable for mutagenesis with the goal to eliminate activity have been described” (mi396 is a highly conserved micro-RNA) (Baum, page 51, lines 29-32).
Thus, it is the Office’s position that any mutation introduced in or adjacent to a miR396 binding site of an endogenous GRF transcription factor gene that disrupts miR396 binding is an obvious variant, as taught by the cited references (Fu and Baum) and the state of the art in general. Although Fu and Baum do not explicitly teach introducing an in-frame mutation, there is no way to distinguish a soybean plant comprising an in-frame mutation from a soybean plant comprising a non-in-frame mutation which disrupts miR396 binding. As such, it would have been obvious to one of ordinary skill in the art to introduce a mutation in the location of the miR396 binding site as taught by Fu and Baum to disrupt DNA binding.
Response to Applicant’s Arguments
Applicant's arguments filed 03/06/2026 have been fully considered but they are not persuasive.
Applicant argues that the combination of Fu and Baum fails to teach or suggest each and every element of the claims.
Fu teaches methods for increasing yield in a plant, the method comprising increasing the expression or levels of a GRF. Fu teaches introducing at least one mutation into a least one nucleic acid encoding a GRF; the mutation is in a miRNA396 binding site; the miR396 binding site (SEQ ID NO: 45) as taught by FU shares 100% sequence identity with instant sequence SEQ ID NO: 109 (miR396 binding site). Fu teaches the mutation is any mutation that prevents the cleavage of the sequence by microRNA and thus its subsequent degradation. Baum teaches methods of interfering with the miRNA396 and GRF interaction, whether by increasing activity of the same, through such mechanisms as overexpression, inhibition of activity, such as through inhibition of translation or transcription, or introduction of heterologous interfering or competing proteins.
Baum teaches all GFR transcription factors will have an miRNA396 sequence and a binding site (the sequences taught by Baum align with the instant sequences); SEQ ID NO: 21, a Glycine max GmGRF9 gene, which shares 100% sequence identity with instant sequence SEQ ID NO: 73; and the protein encoded by Baum sequence SEQ ID NO: 21 shares 100% sequence identity with instant sequence SEQ ID NO: 74 and encompasses instant sequence SEQ ID NO: 110.
Therefore, the combination of Fu and Baum teaches a GRF transcription factor having 100% sequence identity to instant sequence SEQ ID NO: 73; the highly-conserved sequence of an miR396 binding site having 100% sequence identity to instant sequence SEQ ID NO: 109; several options of mutations comprising a base deletion and/or a base insertion in the miR396 binding site; and modulating the miRNA396-GRF interaction in soybean for improved or maintained traits.
Although neither Fu nor Baum explicitly teach an in-frame deletion, it is reiterated that it is the position of this Office that any mutation that disrupts the binding of DNA is rendered obvious by the teachings of FU and Baum.
Summary
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTINA MEADOWS whose telephone number is (703)756-1430. The examiner can normally be reached Monday - Friday 9:00 am - 5:00 pm. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on 571-270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
CHRISTINA MEADOWS
Examiner
Art Unit 1663
/CHRISTINA L MEADOWS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
Prosecution Insights