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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 03February2026 has been entered.
Election/Restrictions
[Copied from Final Action 13November2025→] Applicant’s election without traverse of Group II, (A)(1) and IPA1 gene, (B)(i) SPL, (C) SPL9a (and sequences SEQ ID NOs: 143, 144, 178, and 145), (D)(IV) a mutation in an miR156 binding site located from about nucleotide 6624-6847 (numbered according to SEQ ID NO: 143) in the reply filed on 09Mau2025 is acknowledged. Applicant did not specify a mutant SPL9a sequence for examination1, so the Office presumes Applicant elects the “CE56385” sequence SEQ ID NO: 295 for examination (see claims 66 and 123).2 Claims 1, 4, 13, 17, 19, 31, 34, 35, 45, 97, 100, 114, 117, 118, and 142 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group or species, there being no allowable generic or linking claim. Please also note that claim 54 “orthologue thereof” as well as parts (b) and (c); claim 60 parts (b) and (c); claim 90 parts (b) and (c); claim 102 parts (b)-(f) [both lists]; claim 123 parts (b)-(e); and claim 160 parts (b)-(c) ARE ALSO WITHDRAWN as being directed toward non-elected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09May2025.
Status of the Claims
The amendments and arguments filed 03February2026 are acknowledged and have been fully considered. Claims 2-3, 5-18, 20-44, 46-53, 55-59, 61-62, 64-65, 67-89, 91-101, 103-106, 108-122, 124-159 were previously canceled. Claims 1, 4, 19, 45, 54, 60, 63, 66, 90, 102, 107, 123, 160, 161 are pending. Claims 1, 54, 90, 102, 160 are currently amended. Claims 60, 63, 66, 107, 123, 161 were previously amended. Following the restriction requirement mailed 17April2025 and Applicant’s election dated 09May2025, claims 1, 4, 19, 45 REMAIN withdrawn as being directed toward a non-elected group and/or species (rejoinder currently being inappropriate).
Claims 54(part a), 60(part a), 63, 66(as it relates to elected SPL9), 90(part a), 102(parts a), 107, 123(part a), 160(part a), 161 remain examined on the merits herein.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) [US provisional 63337244 filed 02May2022] is acknowledged. Claims 54(part a), 60(part a), 63, 66(as it relates to elected SPL9), 90(part a), 102(parts a), 107, 123(part a), 160(part a), and 161 MAINTAIN an effective filing date of 02May2022.
Withdrawn Objections and/or Rejections
Rejections made of record in the final office action dated 13November2025 and Advisory Action dated 18December2025 that are not otherwise discussed herein are withdrawn. In particular:
RE ¶ 6: The obviousness rejection over BAO et al. and SUN et al. is withdrawn in view of the claim amendments (adding functional/phenotypic change requirements to claims 54 and 90, to which all claims refer); and
RE ¶ 7: The Utility rejection is withdrawn in view of the claim amendments (adding functional/phenotypic change requirements to claims 54 and 90, to which all claims refer).
Claim Objections
Claims 54 and 90 are objected to because of the following informalities: (1) both of these claims now recite functional/phenotypic changes, but the language used in each claim is different (i.e., inconsistent). For example, claim 54 recites “as compared to a control plant that is devoid of the at least one mutation” whereas claim 90 recites “as compared to a plant or plant part not comprising the same mutation”. Please choose one phraseology and amend the claims so that they are consistent (e.g., either both refer to a “control” or neither refer to a “control”). (2) these claims both need to be amended so that the control plant, or “plant or plant part not comprising the same mutation” is grown in the same environmental conditions (see the specification at page 12, lines 5-6). As confirmed by the specification, it is well understood that growth conditions impact plant phenotypes, so the absence of this clarifying phrase is understood to have been an oversight (= this is presented as an objection and not a rejection). Appropriate correction is required.
Claim Rejections - 35 USC § 112 - Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 54 and 90 (therefore, also claims 60, 63, 66, 102, 107, 123, 160, 161 which refer thereto without correcting the issue) are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
These claims now recite “improved yield trait”. Because “improved” is subjective, these claims are indefinite. Did Applicant perhaps mean to recite “increased”? Please note the Written Description rejection below wherein narrowing amendments are recommended.
Claim Rejections - 35 USC § 101-Utility
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 160 and 161 are rejected under 35 U.S.C. 101 because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility.
Claim 160 (to which claim 161 refers) is amended to recite a guide nucleic acid “that may be used in a gene editing system comprising a CRISPR-Cas effector protein ….” Because the “may be used” language is a non-limiting exemplary, intended use; it does not change the fact that claims 160 and 161 are directed toward guide nucleic acids (noting that “guide” is itself a non-limiting intended use).
There is no disclosed, nor well-recognized, specific or substantial use of a “guide” nucleic acid outside of a gene editing system. Please further amend claim 160 so that the guide nucleic acid is within the gene editing system (Applicant may wish to consider what the Office previously suggested: amending claims 160 and 161 so that they are directed toward a gene editing system that comprises the recited guide nucleic acid).
[This is part of the Utility Rejection’s Form Paragraph, see MPEP § 2107.02 →] Claims 160 and 161 are also rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph. Specifically, because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility for the reasons set forth above, one skilled in the art clearly would not know how to use the claimed invention.
As summarized at MPEP § 2103 (I)(A): “the claimed invention as a whole must be useful. The purpose of [the Utility] requirement is to limit patent protection to inventions that possess a certain level of ‘real world’ value, as opposed to subject matter that represents nothing more than an idea or concept, or is simply a starting point for future investigation or research” (internal citations omitted). See MPEP §§ 2164.01(c) and 2107.01-.03, e.g., 2107.02(III)(A) (“… a specification which contains a disclosure of utility which corresponds in scope to the subject matter sought to be patented must be taken as sufficient to satisfy the utility requirement of § 101 for the entire claimed subject matter unless there is a reason for one skilled in the art to question the objective truth of the statement of utility or its scope.”). See also MPEP § 2107.02(I) (“… where it can be established that other species clearly encompassed by the claim do not have utility should a [utility] rejection be imposed on the generic claim. In such cases, the applicant should be encouraged to amend the generic claim so as to exclude the species that lack utility.”).
Claim Rejections - 35 USC § 112 – Written Description
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 54(part a), 60(part a), 63, 66(as it relates to elected SPL9), 90(part a), 102(parts a), 107, 123(part a), 160(part a), 161 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.
As a reminder, these claims continue to recite non-elected, non-examined subject matter. Only claims 54(part a), 60(part a), 66(as it relates to elected SPL9), 90(part a), 102(parts a), 123(part a), 160(part a) are under examination (claims 63, 107 and 161 do not appear to recite non-elected parts and are, thus, examined in their entirety).
This rejection is necessitated by the amendment to the claims dated 03February2026 whereby functional/phenotypic effects are now required (that the mutation within (elected) SPL9a causes “altered plant architecture” and/or “improved yield trait” as compared to a control plant that is devoid of the mutation).
Executive summary of the issues:
(1) These claims recite any plant, but the limited evidence in the specification and prior art only support claims requiring a soybean plant;
(2) These claims recite a breadth of sequence structures (note the use of “80%” and “90%” sequence identities), but the specification and prior art only support claims requiring 95% or more sequence identity to the listed sequences;
(3) These claims recite any insertion and/or deletion mutation (including any out-of-frame insertion or any out-of-frame deletion [claim 63] and including any in-frame-deletion [claim 107]), but the specification and prior art only support achieving specific functions/phenotypes (see (4) below) via a homozygously present mutant SPL9a allele characterized by having a 9 basepair deletion at the position corresponding to 6720 of the sequence SEQ ID NO: 295 (i.e., the elected CE56385 species currently under examination);
(4) These claims recite a function/phenotype change being any “altered plant architecture” and/or any “improved yield trait” (which encompasses any increase in any yield trait, see the Indefiniteness rejection of this language hereinabove), but the specification and prior art only support generating a specifically modified soybean plant (see (3) above) that has, a result of that modification, increased pods on main stem and/or pods per node main stem as compared to a wild type control plant devoid of the mutation and grown in the same environmental conditions.
With respect to the elected, examined SPL9a mutant [soybean] plant referred to as “CE56385”, Examples 2 and 8 of the specification are relevant. In the absence of further information from Applicant (such as declaration practice, which has been recommended of record), and given only means/averages and standard deviation values for E2 soybean plants (Example 8 at pages 108-109 of the specification, Tables 9-10); the Office has generated charts with accompanying 2x Standard Error of the Mean (SE) error bars (below) to make it clear on the record that there is no statistically significant difference between the wild type control group’s phenotypes as compared to the elected CE56385 group’s phenotypes for 6 of the 8 assayed phenotypes: nodes on main stem, branches per plant, pods on branches, pods per plant, seeds per plant, and seeds per pod (shown in the below charts via overlapping 2xSE error bars, where the overlap is unclear a horizontal line has been provided for ease of review). The only 2 assayed phenotypes that do appear to have a statistically significant difference (between wild type control group and the elected CE56385 group) are pods on main stem and pods per node main stem (denoted in the below charts by open boxes). To ensure a clear record, please see CUMMING et al.3 for a description of 2xSE error bars and how to interpret error bars generally (in brief, 2xSE error bars may be used for an approximation of p-value and when 2xSE error bars touch or overlap, that generally means that the difference between the means/averages is not statistically significant (i.e., p > 0.05)). To be clear, the Office focused on the E2 generation (Example 8) at least because the data for E1 plants (Example 2, Table 3 at pages 104-105 of the specification) is incomplete (e.g., without both mean/average and standard deviation information, SE error bars (and 2xSE error bars) cannot be generated. The charts below show that, even for the elected CE56385 plants characterized by a homozygously present, 9 basepair, in-frame deletion in SPL9a (corresponding to position 6720 of SEQ ID NO: 295)4, Applicant has not shown that “altered plant architecture and/or improved yield trait(s)” as compared to a control plant can actually be achieved. At most, Applicant has only shown that pods on main stem and pods per node main stem are increased (there is currently no evidence of record to support any alteration to any plant architecture or any “improved” (increase?) to any yield trait). The currently claimed functions/phenotypes are much broader than what is supported by the specification and prior art.
The prior art does not supplement the deficiencies of this specification. BAO et al. and SUN et al. (discussed of record with respect to obviousness) are relevant to these claims in terms of modifying SPL9 in soybean, but neither can account for the function/phenotype changes now recited in these claims. As said of record, BAO et al. and SUN et al. both teach increasing SPL9 by decreasing suppression thereof (BAO et al. increase SPL9a via mutating the SPL9b suppressor, SUN et al. increase SPL9d by mutating the binding site of the miR156 suppressor). Notably, BAO et al. specifically observed that plants with increased SPL9a (via decreased SPL9b suppression) "showed comparable plant architecture as [wild type] plants"5. Therefore, a skilled artisan would not reasonably expand the specification’s showing of “increased pods on main stem and/or increased pods per node main stem” out to any altered plant architecture or any improved (increased?) yield trait in view of the prior art (including in view of BAO et al. and SUN et al.). In fact, BAO et al. evidences that the full breadth of the claimed function/phenotype changes cannot be achieved and they certain cannot be achieved with the full breadth of mutations being claimed, the full breadth of sequence structures being claimed, or in any plant type.
It follows that Applicant has not shown that the full breadth of structures being claimed will actually achieve “altered plant architecture and/or improved yield trait(s)” as compared to a control plant. Absent evidence to the contrary (e.g., data and/or data analysis submitted via declaration practice), a skilled artisan at the time this application was filed would not reasonably recognize Applicant as having possession of the full metes and bounds of what is being claimed. It would be remedial of this rejection to amend the claims so that they require: a soybean plant homozygously comprising a modified SPL9a characterized by having a 9 basepair deletion at the position corresponding to 6720 of the sequence SEQ ID NO: 295 and wherein the soybean plant exhibits increased pods on main stem and/or pods per node main stem as compared to a wild type control plant devoid of the mutation and grown in the same environmental conditions.
Charts Including 2xSE Error Bars for Results in Tables 9 and 10 (Example 8)—Input data follows:
PNG
media_image1.png
351
312
media_image1.png
Greyscale
PNG
media_image2.png
347
318
media_image2.png
Greyscale
PNG
media_image3.png
348
311
media_image3.png
Greyscale
PNG
media_image4.png
376
323
media_image4.png
Greyscale
PNG
media_image5.png
347
356
media_image5.png
Greyscale
PNG
media_image6.png
330
297
media_image6.png
Greyscale
PNG
media_image7.png
313
299
media_image7.png
Greyscale
PNG
media_image8.png
312
272
media_image8.png
Greyscale
Table 9 Nodes on Main Stem
Wild Type Control
CE56385 E2
Average
18.7
18.4
Standard Error of the Mean (SE)
0.138
0.183
2xSE
0.276
0.366
Table 9 Branches Per Plant
Wild Type Control
CE56385 E2
Average
15.2
14.4
Standard Error of the Mean (SE)
0.447
0.447
2xSE
0.894
0.894
Table 9 Pods on Branches
Wild Type Control
CE56385 E2
Average
115.4
113.8
Standard Error of the Mean (SE)
5.63
4.59
2xSE
11.26
9.18
Table 9 Pods on Main Stem
Wild Type Control
CE56385 E2
Average
38.3
56.4
Standard Error of the Mean (SE)
1.97
2.29
2xSE
3.94
4.58
Table 10 Pods Per Node Main Stem
Wild Type Control
CE56385 E2
Average
2
3
Standard Error of the Mean (SE)
0.112
0.109
2xSE
0.224
0.218
Table 10 Pods Per Plant
Wild Type Control
CE56385 E2
Average
153.7
170.2
Standard Error of the Mean (SE)
5.55
5.57
2xSE
11.1
11.14
Table 10 Seeds Per Plant
Wild Type Control
CE56385 E2
Average
264.4
307
Standard Error of the Mean (SE)
11.61
14.99
2xSE
23.22
29.98
Table 10 Seeds Per Pod
Wild Type Control
CE56385 E2
Average
1.7
1.9
Standard Error of the Mean (SE)
0.067
0.066
2xSE
0.134
0.132
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Rebecca STEPHENS whose telephone number is (571)272-0070. The examiner can normally be reached Monday through Friday 8:30-4:30.
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 at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/REBECCA STEPHENS/Examiner, Art Unit 1663
/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
1 See part (D) of the Election of Species (page 5) dated 17April2025.
2 For the sake of a clear record, please note that the “CE52366” embodiment in the specification comprises a SPL9a mutation (in combination with an SPL9b mutation) and is represented by SEQ ID NO: 300.
3 See CUMMING et al. “Error bars in experimental biology” 2007 J. Cell Biology 177(1):7-11.
4 Specification at page 103 describing the modified soybean plant referred to as “CE56385”.
5 BAO et al. at page 7, right column and Figure S5.