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 .
Claim Status
The Applicant cancelled claims 13-14 and 16-17.
Claims 7-10 are pending and 15 are being examined.
All previous objections and rejections not set forth below have been withdrawn in view of applicant’s amendments to the claims.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 7-10 and 15 remain rejected under 35 U.S.C. 103 as being unpatentable over Ping et al. (Dt2 Is a Gain-of-Function MADS-Domain Factor Gene That Specifies Semideterminacy in Soybean, 2014, The Plant Cell, 26:2831–2842) in view of Kou et al. (Natural variation of the Dt2 promoter controls plant height and node number in semi‑determinant soybean, 2021, Mol. Breeding, 41: 40) and Jacobs et al. (Targeted genome modifications in soybean with CRISPR/Cas9, 2015, BMC Biotechnology, 15:1-10), in evidence of Wang et al. (GmSnRK1.1, a Sucrose Non-fermenting-1(SNF1)-Related Protein Kinase, Promotes Soybean Resistance to Phytophthora sojae, 2019, Front. Plant Sci. 10:996) and Xu et al. (Responses of Branch Number and Yield Component of Soybean Cultivars Tested in Different Planting Densities, 2021, 11:69).
Due to applicant’s amendments, the rejection is modified from the rejection set forth on pages 5-9 in the Office action dated 4/7/2026.
Claim 7 is drawn to a method for improving yield of legume or increase in branch numbers of legume of the soybean variety DN50 by inactivating the function of a gene encoding SEQ ID NO: 4.
Ping et al. describes Soybean (Glycine max) stem growth habit is a key adaptation and
agronomic trait that directly affects soybean yield among many other traits (page 2831, left column, para 1, line 1-5). Ping et al. teaches a Shoot Identity 2 (DT2) gene in soybean, which is a legume. The genomic DNA sequence encoding the MADS-box protein DT2 (GenBank Accession No. KF908015) encodes a mRNA sequence which is having 100% sequence identity to SEQ ID NO. 4, as discussed in the previous Office action dated 04/09/2025 (page 4-8). Ping et al. describes that Dt2 is a relatively new gain-of-function mutation which occurred after the domestication of cultivated soybeans (page 2838, left column, para 1, line 6-7). Dt2 protein represses the expression of Dt1 gene (abstract, line 8-9; page 2838, left column, para 1, last 3 lines).
However, Ping et al. does not explicitly or directly connect downregulation, silencing, knock-out or inactivation of the Dt2 gene with either yield or branch number.
Kou et al. describes that lower expression of Dt2 gene in soybean releases the inhibition (repression) of Dt1 expression which increases number of nodes and grain yield (abstract).
Before the effective filing date of the invention, it would have been obvious to the ordinarily skilled artisan to downregulate or inactivate the Dt2 gene, as described by Kou et al., to relieve the Dt2-mediated repression of Dt1 gene, as described by Ping et al. and Kou et al, in the approved soybean variety DN50, which is routinely used for gene transformation experiments, as evidenced by Wang et al. (page 2, right column, para 3, line 5-6).
Before the effective filing date, an ordinarily skilled artisan would have been motivated to inactivate the Dt2 gene in the elite soybean variety DN50 to increase yield and/or increase branch numbers which is directly correlated to number of nodes, as described by Xu et al. (page 10, para 2, line 1-5).
Regarding claim 8 and 15, gene inactivation by knocking out is a well-known standard process in the art, as described by Jacobs et al. (abstract).
Jacobs et al. describes a highly specific genome editing tool in soybean by using CRISPR-Cas9 based targeted gene editing technique comprising a guide RNA (sgRNA or gRNA) as (page 1, abstract; left column, last para). sgRNA reads on to sgRNA, as described by the Applicant (spec, page 5, para 4, line 1-2). Jacobs et al. also describes developing a vector system to simplify the production of CRISPR/Cas9 targeting vectors, which is applicable for targeting any gene in a plant including soybean (page 1, abstract) to produce a variety of mutations including deletions, SNPs, insertions, and replacements (page 3, left column, para 3, line 5-7) and, thus can inactive one (page 3, left column, para 3, line 1-3) (as recited in claim 8) or more (page 3, left column, para 4, line 1-9) (as recited in claim 9) target gene(s) in the plant using one or more gRNAs, as needed. In plants, such targeted genome editing is a standard practice and used to knockout genes, modify gene expression by disrupting promoter sequences, or insert transgenes at a specific location via homologous recombination (page 1, right column, para 2). Jacobs et al. also describes more than one gRNA target sequences (page 8, left column, para 1) cloned in expression vectors comprising Kanamycin (nptII) and Hygromycin (hpt) antibiotic resistance markers (Jacobs et al., 2015, additional file 6), used in Agrobacterium mediated transformation including using Agrobacterium tumefaciens (page 6, right column, para 1) (cf. instant claim 8). Jacobs et al. also describes the process and the requirements to design the gRNA sequence(s) comprising about 20 bp, including 22-23 bp, sequence homology with the coding region of specific target gene(s) (page 1, right column, para 1; page 7, right column, last para). Choosing any specific sequence in the target gene within its coding region containing about a 20 nucleotide stretch of homology to design the guide RNA sequence, as described by Jacobs et al., is within the experimental design choice of an ordinarily skilled artisan without altering the outcome. It would have been obvious to a person of ordinary skill in the art to choose about 20 bp long gRNA sequence comprising instant SEQ ID NOs: 9 or 10 (as recited in claim 10) mutate and, thus, inactivate the Dt2 gene.
Moreover, designing specific gRNA sequence is a routine standard practice in the art especially if the target sequence comprising the coding sequence (cDNA sequence) of the target gene is already known. It is noted that instant SEQ ID NO: 4 encoding the cDNA of Dt2 gene has 100% sequence identity to instant SEQ ID NOs: 9-10 (data not shown).
Before the effective filing date of the invention, it would have been obvious to a person with ordinary skill in the art to inactivate the function of the Dt2 gene encoding the cDNA sequence consisting of SEQ ID NO. 4 in DN50 soybean variety, as described by Ping et al. in view of Kato et al. and in evidence of Wang et al., by using CRISPER/Cas9 gene editing technique comprising a suitable gRNA, as taught by Jacobs et al., to transform the growth habit of the DN50 soybean plants to indeterminate type, as described by Ping et al. in view of Kato et al. and in evidence of Wang et al.
Before the effective filing date of the instant invention, a person with ordinary skill in the art would have been motivated to knockout or inactivate the Dt2 gene in the established DN50 soybean variety with a realistic goal to transform it into an indeterminate type to increase yield and branch number.
Response to Applicant’s Arguments
The response from the Applicant dated 7/7/2026 is fully considered but not found persuasive.
Regarding the rejections under 35 U.S.C. § 103, the Applicant argues, “Kou found that differences in plant height, node number, and grain yield between these two semi-determinate varieties arise from polymorphisms in the Dt2 promoter that cause differences in expression level of Dt2- not from the presence or absence of Dt2 function” (response, p.7, last para, line 2-5). The Applicant continues to argue, “the claimed methods produce legumes with unexpected and superior properties that could not have been predicted by the cited prior art” (response, p.9, para 2) and “Xu does not teach that increasing yield is always directly correlated with increasing branch number and node number" (response p.10, para 4, line 1-2). The Applicant alleges, “the prior art as a whole (Ping, Kou, and Xu) does not teach that one could reasonably expect to increase branch number and yield by knocking out Dt2 in soybean variety DN50 (response, p.12, para 1, line 1-3).
The Examiner disagrees. Claim 7 recites “… inactivating the function of a gene….” and does not require “presence or absence of Dt2 function” (i.e., the function of the Dt2 protein), as asserted by the Applicant. The “function” of a gene comprises its pattern and/or level of expression. The Applicant does not define the term “inactivation”. The Examiner interprets that inactivating the function of a gene includes reducing or downregulating the expression of the gene.
Moreover, an ordinarily skilled artisan would reasonably expect to enhance the trait(s), i.e., expressivity of the trait(s), conferred by downregulation of a gene by knocking out the gene altogether, especially if the gene and/or the gene product (the protein encoded by the gene) acts as a repressor (an inhibitor) of a (target or desirable) trait. Dt2 gene acts as a repressor for Dt1 gene, as taught by Ping et al. and Kou et al. (as discussed above). Thus, an ordinarily skilled artisan would have been motivated to silence or knockout Dt2 gene expression (thus, no Dt2 protein activity) with a reasonable expectation of success to enhance the release of the inhibition (repression) of Dt1 expression enhancing the expression of Dt1 protein, which is known to increase grain yield in soybean, as described by Kou et al. (abstract). Thus, the result of the instant invention is neither unexpected nor superior.
Claim 7 does not require increasing yield and branch number (and/or node number) but recites “improving yield of legume or increasing branch numbers”. However, suppressing or inactivating the Dt2 gene (as described by Kou et al.) would release the inhibition of the Dt1 gene in the elite soybean variety DN50 resulting in increase in both yield and branch numbers, as increased node number (NN) (as described by Kou et al.; abstract, right column, line 12-14) is directly correlated to increased branch numbers, as described by Xu et al. (page 10, para 2, line 1-5).
Conclusion
All claims are rejected.
THIS ACTION IS MADE FINAL. 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.
Communication
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
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