DETAILED ACTION
Applicant's submission filed on September 29, 2025 has been entered.
Claims 2-3 and 5-13 are cancelled.
Claims 1, 4, and 14-20 are pending.
Claims 1 and 20 are currently amended.
Claims 4 and 19 are withdrawn, currently amended.
Claims 14-18 are withdrawn.
Claims 1 and 20 are examined.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
All previous objections and rejections not set forth below have been withdrawn.
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 .
Withdrawn Rejections
The rejection of claim 1 on the judicially-created basis that it contains an improper Markush grouping of alternatives is withdrawn in light of the amendment of claim 1.
The rejection of claims 1 and 20 under 35 U.S.C. 103 as being unpatentable over Ge et al. (U.S. Patent No. 10,087,458, issued Oct. 2, 2018) in view of Yang et al. (U.S. Patent No. 10,308,947, issued Jun. 4, 2019) and Chen et al. (GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem. Biophys. Res. Commun. 2007 Feb 9;353(2):299-305. Epub 2006 Dec 13) is withdrawn in light of the claim amendments.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1 and 20 are 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.
Claim 1 as currently amended is drawn to a modified soybean cell, wherein the modified soybean cell comprises one targeted modification, wherein the one targeted modifications occurs in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene, and wherein the targeted modification knocks out expression of the gene, and wherein a soybean plant comprising the modified soybean cell has increased seed weight and/or seed size relative to a soybean plant lacking the modification.
Claim 20 as currently amended is drawn to a modified soybean plant comprising the modified soybean cell of claim 1, or a progeny plant or progeny seed of the modified soybean plant, wherein cells of the modified soybean plant, progeny plant, or progeny seed comprise the targeted modification.
The specification does not identify any specific soybean gene as causing increased seed weight and/or seed size upon the gene or genes being specifically modified. Accordingly, a modified soybean cell, wherein the modified soybean cell comprises one targeted modification, wherein the one targeted modifications occurs in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene, and wherein the targeted modification knocks out expression of the gene, and wherein a soybean plant comprising the modified soybean cell has increased seed weight and/or seed size relative to a soybean plant lacking the modification, does not find support in the specification, and thus constitutes new matter.
Furthermore, the claimed composition itself is not adequately described. The specification does not describe any soybean plant that has increased seed weight and/or seed size and that comprises a modified soybean cell comprising one targeted modification, wherein the one targeted modifications occurs in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene, and wherein the targeted modification knocks out expression of the gene. Nor does the specification describe what type of modification to make in a gene having at least 95% sequence identity to SEQ ID NO: 416 such that a soybean plant that comprises a soybean cell having this modification will exhibit increased seed weight and/or seed size relative to a soybean plant lacking these modifications. Accordingly, one skilled in the art would not recognize that the applicant was in possession of the claimed invention as a whole at the time of filing, and Applicant has not described a representative number of species falling within the scope of the required genus of modified soybean cells, or the structural features unique to the genus that are correlated with increased seed weight and/or seed size.
Response to Arguments
Applicant's arguments filed September 29, 2025 have been fully considered but they are not persuasive.
Applicant maintains that the rejection is rendered moot by the amendment of claim 1.
Applicant's arguments are not persuasive.
Applicant's arguments are not persuasive because the amendment of claim 1 does not render the rejection moot, because the specification does not describe any soybean plant that has increased seed weight and/or seed size and that comprises a modified soybean cell comprising one targeted modification, wherein the one targeted modifications occurs in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene, and wherein the targeted modification knocks out expression of the gene. Accordingly the rejection is maintained.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ge et al. (U.S. Patent No. 10,087,458, issued Oct. 2, 2018) in view of Feitelson et. al. (U.S. Patent No. 10,973,187, issued Apr. 13, 2021).
Claim 1 as currently amended is drawn to a modified soybean cell, wherein the modified soybean cell comprises one targeted modification, wherein the one targeted modifications occurs in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene, and wherein the targeted modification knocks out expression of the gene, and wherein a soybean plant comprising the modified soybean cell has increased seed weight and/or seed size relative to a soybean plant lacking the modification.
Claim 20 as currently amended is drawn to a modified soybean plant comprising the modified soybean cell of claim 1, or a progeny plant or progeny seed of the modified soybean plant, wherein cells of the modified soybean plant, progeny plant, or progeny seed comprise the targeted modification.
Ge et al. teach a forage plant cell and plant modified to decrease or knock out the expression of the gene BS1 (BIG SEEDS1) using an antisense or RNAi construct (columns 22-36; claims 1-10). Ge et al. also teach that the soybean forage plant gene BS1 (BIG SEEDS1) encodes a protein having the amino acid sequence of SEQ ID NO: 637, the same protein encoded by a gene having the nucleotide sequence of SEQ ID NO: 416 (page 141, Table 10) - see sequence alignment below. Ge et al. additionally teach that decreasing or knocking out the expression of the gene BS1 (BIG SEEDS1) improves forage quality, increases plant biomass and seed yield (columns 22-36; claims 1, 5).
Ge et al. do not teach a soybean cell comprising a targeted modification in a gene having at least 95% sequence identity to SEQ ID NO: 416 or in a regulatory sequence affecting the expression of the gene wherein the targeted modification knocks out expression of the gene.
Feitelson et. al. teach a plant cell modified to decrease or knock out the expression of the gene encoding deoxyhypusine synthase (DHS) using an antisense construct, wherein a plant comprising the modified plant cell has increased seed yield (paragraph spanning columns 2-3). Feitelson et. al. also teach a plant cell modified to decrease or knock out the activity of the product of the gene encoding DHS by modifying the DHS gene using gene editing technology (CRISPR), wherein a plant comprising the modified plant cell has increased seed size (column 25 first full paragraph).
Given the teachings of Ge et al. that a forage plant cell and plant can be modified to decrease or knock out the expression of the gene BS1 (BIG SEEDS1) using an antisense or RNAi construct, including a soybean forage plant gene BS1 (BIG SEEDS1), and that decreasing or knocking out the expression of the gene BS1 (BIG SEEDS1) improves forage quality, increases plant biomass and seed yield, and given the teachings of Feitelson et. al. that a gene that affects seed yield and size can be downregulated using alternative technologies such as antisense technology or gene editing technology to produce a plant that has increased seed yield or size, it would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify a soybean cell and plant to comprise a targeted modification that occurs in a BS1 (BIG SEEDS1) gene wherein the targeted modification decreases or knocks out expression of the BS1 (BIG SEEDS1) gene.
One skilled in the art would have been motivated to do so in order to improve the forage quality, and increase the biomass and seed yield of a soybean plant comprising the targeted modification. One skilled in the art would have had a reasonable expectation of success, given the success of Ge et al. in improving the forage quality, and increasing the biomass and seed yield of forage plants comprising a modified or suppressed BS1 (BIG SEEDS1) gene using antisense or RNAi technology, and given the success of Feitelson et. al. and others in downregulating a DHS gene using alternative technologies such as antisense technology and gene editing technology to produce a plant that has increased seed yield or size.
Thus the claimed invention would have been prima facie obvious as a whole to a person having ordinary skill in the art before the effective filing date of the claimed invention.
Response to Arguments
Applicant's arguments filed September 29, 2025, directed to the prior rejection of claims 1 and 20 under 35 U.S.C. 103 as being unpatentable over Ge et al. in view of Yang et al. and Chen et al., now withdrawn, have been considered with respect to the currently applied reference of Ge et al., but they are not persuasive.
Applicant maintains that the Examples of Ge do not provide any data showing that decreasing or knocking out the expression of the soybean BS1 gene alone is sufficient to improve forage quality, increase plant biomass and seed yield in soybean.
Applicant points to Example 13 of Ge, where an artificial microRNA was designed to target a highly conserved coding sequence of GmBS1 (Glyma10g38970) and GmBS2 (Glyma20g28840), and Applicant notes that Ge discloses that transgenic soybean plants transformed with the artificial microRNA, in which both GmBS1 and GmBS2 were downregulated, displayed increased sizes and weights of seeds, seed pods, and leaves as compared with wild-type plants. Applicant maintains that the Examples of Ge do not describe a soybean plant in which the expression of either GmBS1 or GmBS2 is downregulated individually.
Applicant also maintains that one skilled in the art would not have had a reasonable expectation that eliminating expression of GmBS1 alone would have a similar effect on soybean seed size due to the potential functional redundancy of GmBS1 and GmBS2 in soybean. Applicant points out that in Ge at Example 10 two tandem repeat genes related to BS1 in Arabidopsis, At4g14713 (PPD 1) and At4g14720 (PPD2) were evaluated, and Ge specifically notes that the single ppd mutants displayed weaker phenotypes than the double deletion mutant due to functional redundancy, and Applicant maintains that in the case of GmBS1 and GmBS2, one would similarly expect functional redundancy, meaning both genes would need to be simultaneously downregulated to produce a significant phenotype. Applicant also maintains that the fact that Ge downregulated both GmBS1 and GmBS2 genes together strongly suggests that they anticipated such functional redundancy between these genes, and that Ge therefore does not provide any motivation or rationale for targeting GmBS1 independently of GmBS2.
Applicant's arguments are not persuasive.
With respect to Applicant’s assertion that the claimed invention is not rendered obvious because the Examples of Ge do not provide any data showing that decreasing or knocking out the expression of the soybean BS1 gene alone is sufficient to improve forage quality, increase plant biomass and seed yield in soybean, this is not persuasive. Ge need not provide such data in order to render the claimed invention obvious, because obviousness requires only a reasonable expectation of success. In this regard the Examiner maintains that the data that is provided by Ge is sufficient to provide a reasonable expectation of success, since Ge disclose data on mutagenized plants (Medicago trunculata and Arabidopsis thaliana) that have mutations in individual BS1 genes, in addition to data based on RNAi expression.
With respect to Applicant’s reliance on Example 13 of Ge, this is not persuasive because the rejection does not rely solely on Example 13 of Ge. The rejection relies on the totality of the teachings of Ge, as well as the claims of Ge.
With respect to Applicant’s assertion that one skilled in the art would not have had a reasonable expectation that eliminating expression of GmBS1 alone would have a similar effect on soybean seed size due to the potential functional redundancy of GmBS1 and GmBS2 in soybean, this is not persuasive. The Examiner reiterates that the data that is provided by Ge is sufficient to provide a reasonable expectation of success. Regarding Applicant’s assertion that the two soybean genes GmBS1 and GmBS2 would need to be simultaneously downregulated to produce a significant phenotype because Arabidopsis single mutants PPD1 and PPD2 displayed weaker phenotypes than the double PPD1/PPD2 mutant due to the functional redundancy of PPD1 and PPD2, this is not persuasive, because absent evidence to the contrary, a weaker phenotype is not insignificant. The Examiner maintains that the display of weaker phenotypes by Arabidopsis single mutants PPD1 and PPD2 is sufficient to provide a reasonable expectation of success that targeting a single BS1 gene could produce the desired phenotype.
Accordingly, the rejection is maintained.
Sequence alignment between SEQ ID NO: 162 of Ge et al. and SEQ ID NO: 637 of the instant application, SEQ ID NO: 637 of the instant application being the protein encoded by a gene having the nucleotide sequence of SEQ ID NO: 416 (page 141, Table 10):
RESULT 1
US-14-861-980A-162
(NOTE: this sequence has 2 duplicates in the database searched.
See complete list at the end of this report)
Sequence 162, US/14861980A
Patent No. 10087458
GENERAL INFORMATION
APPLICANT: The Samuel Roberts Noble Foundation, Inc.
TITLE OF INVENTION: Manipulating BS1 for Plant Seed Yield
FILE REFERENCE: NBLE:090US
CURRENT APPLICATION NUMBER: US/14/861,980A
CURRENT FILING DATE: 2015-09-22
PRIOR APPLICATION NUMBER: 62/055,498
PRIOR FILING DATE: 2014-09-25
NUMBER OF SEQ ID NOS: 177
SEQ ID NO 162
LENGTH: 346
TYPE: PRT
ORGANISM: Glycine max
Query Match 100.0%; Score 1808; Length 346;
Best Local Similarity 100.0%;
Matches 346; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MNGGATTATFRSILDKPLNQLTEDDISQLTREDCRRFLKEKGMRRPSWNKSQAIQQVISL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MNGGATTATFRSILDKPLNQLTEDDISQLTREDCRRFLKEKGMRRPSWNKSQAIQQVISL 60
Qy 61 KALLEPSDDDTPPPPPPAMHHRSHAQPQPQVNLSEPPPPPPKAPPPEEPAFHAAEDIQKS 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 KALLEPSDDDTPPPPPPAMHHRSHAQPQPQVNLSEPPPPPPKAPPPEEPAFHAAEDIQKS 120
Qy 121 ASSGEKPTETNDTNTNVASPKGCATSGSFGQMTIFYCGKVNVYDRVSPDKARAIMQLATS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ASSGEKPTETNDTNTNVASPKGCATSGSFGQMTIFYCGKVNVYDRVSPDKARAIMQLATS 180
Qy 181 PVQLTQDDPLNGNAAVWTSPCHLPMDKDVLVPVDTTILQVAQADKMVEYPLQYREKGSIA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PVQLTQDDPLNGNAAVWTSPCHLPMDKDVLVPVDTTILQVAQADKMVEYPLQYREKGSIA 240
Qy 241 RDADVEGQEHRKVSLQRYLEKRKDRGRLKGKKLTGITSSNFEMYLNLPVKVHSSNGNSSR 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 RDADVEGQEHRKVSLQRYLEKRKDRGRLKGKKLTGITSSNFEMYLNLPVKVHSSNGNSSR 300
Qy 301 SSTSSPPQPRLPLVSSGSDQLKVALPIDLNDKVSLQMFKNAKIQTR 346
||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SSTSSPPQPRLPLVSSGSDQLKVALPIDLNDKVSLQMFKNAKIQTR 346
Conclusion
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.
Remarks
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA E COLLINS whose telephone number is (571)272-0794. The examiner can normally be reached M-F 8:30 am - 5:00 pm.
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/CYNTHIA E COLLINS/Primary Examiner, Art Unit 1662