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 .
Second Non-final Office Action
In response to the information presented during the examiner initiated interview dated 12/12/2025, the office is presenting new grounds of rejection in this second non-final office action.
Claim Status
Claims 1-13 are pending.
Claims 1 and 13 are newly amended.
Claims 1-13 are rejected.
Response to Applicant Arguments – Indefiniteness
In response to applicant arguments and amendments dated 08/25/2025, the indefiniteness rejections of record are withdrawn.
Response to Applicant Arguments – Enablement
In response to applicant arguments and amendments dated 08/25/2025, the enablement rejections of record are withdrawn.
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.
Claims 1-13 are rejected under 35 U.S.C. 103 as being unpatentable over Borchardt, EP 3571925 A1, Published 11/27/2019 in view of Cui, US 9,540,655 B2, patented January 10, 2017 as evidenced by Elsner, WO 2024/018016, Published January 25, 2024.
Independent claim 1 is drawn to a DNA molecule comprising a modified DAS44406-6 transgenic locus. This modified transgenic locus is set forth in SEQ ID NO: 61 and is a 4 base pair deletion in the downstream region flanking the DAS44406-6 transgene. As such this deletion is found in endogenous soybean DNA. Applicant provides information on this sequence in the remarks dated 8/25/2025, specifically, Applicant states the following with respect to the deletions in SEQ ID NO: 61:
“the unique deletion junctions of the disclosure, such as those in SEQ ID NO: 61 serve to improve identification of germplasm, plant cells, plants, and plant parts (including seeds) where the modified INHT26 transgene has been introgressed, and to further distinguish that INHT26-containing germplasm, plant cells, plants and plant parts from those containing the unmodified transgene” (Remarks, Paragraph spanning pages 10-11).
Stated differently, applicant urges that the 4 base pair deletion found in the sequence of SEQ ID NO: 61 can be introduced into plants so that plants comprising that deletion can be more easily identified. This raises questions about the use and function of this invention, specifically, when the invention is used by itself what function does this sequence having this specific deletion have. The office asked Applicant this question in an interview on 12/12/2025, see attached interview summary record dated 12/16/2025, in response Applicant stated that this invention had no other use by itself beyond the generic utility for identifying the modified locus.
Given this, the broadest reasonable interpretation of claim 1 is drawn to a DAS44406-6 soybean transgenic locus comprising a modification to introduce a generic marker sequence wherein the modified locus comprises the sequence of instant SEQ ID NO: 61.
With respect to claim 1, Borchardt teaches a method for making an artificial marker allele for the identification of a nucleic acid of interest preferably encoding a polypeptide conferring a trait of interest, comprising the steps of identifying at least one genomic locus in the target genome which is genetically linked to a nucleic acid of interest and introducing at least one insertion or deletion modification into that target locus (Borchardt, Page 148, Claim 1).
Borchardt clarifies this method in claim 8 on page 148, which states that the insertion or deletion of any of the preceding methods, including the method of claim 1, comprises a deletion in the range of 1-60 contiguous base pairs. In claim 10 on page 148, Borchardt provides further clarification of this method. This claims states “The method according to any preceding claim, wherein said nucleic acid of interest may be an endogenous gene, a heterologous gene, a mutated gene, a transgenic gene or a modified gene introduced or generated by gene editing or base editing”.
Further, Borchardt teaches that providing artificial marker alleles would be advantageous in plant breeding for crop improvement (Borchardt, Page 2, Paragraphs 0007 and 0002). To this end Borchardt teaches that the target plant can be selected from a group including Glycine max (Soybean) and that the trait of interest can be herbicide tolerance which is a typical trait of interest (Borchardt, Page 5, Paragraph 0032; Borchardt, Page 4, Paragraph 0020). Finally, Borchardt teaches that introducing the marker into the target locus can be carried out using CRISPR systems, preferably the CRISPR/Cas9 or CRISPR/Cpf1 systems (Borchardt, Page 7, Paragraphs 0045 and 0047).
In summary, Borchardt teaches methods for making an artificial marker allele for the identification of a transgene encoding traits including herbicide tolerance, in crop plants including soybean through the use of gene editing to introduce a deletion of between 1 and 60 contiguous nucleotides that is linked to the transgene encoding the trait of interest (herbicide tolerance).
With respect to claim 1, Borchardt does not teach making a deletion in the 3’ flanking region of the DAS44406-6 transgenic locus, wherein the resulting modified transgenic locus has the sequence of instant SEQ ID NO: 61.
With respect to claim 1, Cui teaches the soybean event pDAB8264.44.06, which confers resistance to glyphosate, aryloxyalkanoate, and glufosinate herbicides (Cui, Abstract). Elsner provides evidence of an intrinsic characteristic of the teachings of Cui, specifically, Elsner makes clear that the pDAB8264.44.06.1 event of Cui is also known as DAS44406-6 (Elsner, Page 27, Line 2; Elsner, Page 26, Lines 32-33). Further, Cui teaches transgenic soybean plant cells, plant parts and seeds comprising the transgenic event (Cui, Columns 117-118, Claims 1-2 and 9).
It would have been obvious at the time of filing to modify the method of Borchardt to generate an artificial marker allele linked to the DAS44406-6 event of Cui as evidenced by Elsner because this would be applying a known technique to a known device ready for improvement to yield predictable results.
This rationale requires resolving the following Graham factual inquiries (MPEP 2143 D):
a finding that the prior art contained a “base” device (method, or product) upon which the claimed invention can be seen as an “improvement”;
a finding that the prior art contained a known technique that is applicable to the base device (method, or product);
a finding that one of ordinary skill in the art would have recognized that applying the known technique would have yielded predictable results and resulted in an improved system; and
whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness.
Addressing these inquiries one by one, Cui teaches a base device upon which the claimed invention can be seen as an “improvement”. Specifically Cui teaches soybeans containing the DAS44406-6. In fact the only distinction between the claimed invention and the soybeans of Cui is a 4 base pair deletion in the genomic soybean DNA flanking the transgene. Applicant made clear in the interview on 12/12/2025 and in the remarks dated 8/25/2025 that this deletion acts as a generic marker allowing sequences comprising this deletion to be identified, further Applicant stated that by itself this sequence has no function other than as a generic marker, see attached interview summary and the paragraph spanning pages 10-11 of Applicant’s Remarks dated 8/25/2025.
At the time of filing Borchardt taught a method of creating artificial marker alleles for traits of interest which include traits carried on transgenes and herbicide tolerance. These marker alleles can be created through the introduction of 1-60 base pair deletions in sequences linked to the trait of interest. Further Borchardt teaches that these methods are applicable to crop plants including soybean plants. Therefore, at the time of filing there was a finding that there was a known technique for creating artificial marker alleles linked to transgenes conferring traits of interest including herbicide tolerance. The base invention taught by Cui is a soybean plant comprising herbicide tolerance traits conferred by a transgene. Therefore the method of Borchardt is applicable to the base invention of Cui.
Third, at the time of filing a person having ordinary skill in the art would have recognized that applying the known technique of Borchardt to the transgenic soybean plants of Cui would have had the predictable result of producing a unique marker allele of the DAS44406-6 transgenic event that would allow for easy screening for this unique allele and correspondingly the transgenic event.
This would have had a predictable result because the techniques used in the method of Borchardt, specifically gene editing using the CRISPR/Cas system are well known in the art. These techniques are known for their applicability to a wide variety of organisms, accuracy, ease of use, and predictability in generating targeted modifications to a sequence. Given that the target sequence was taught by Cui and known in the art at the time of filing and that the unique marker alleles of Borchardt can be introduced using the CRISPR/Cas system, at the time of filing, the ordinary artisan would have recognized that applying the known technique would have yielded predictable results and resulted in an improved transgenic soybean plant.
Given, that applicant’s invention is a generic marker allele and that the combined teachings of Borchardt in view of Cui as evidenced by Elsner teach soybean plants having unique marker alleles linked to transgenes that are produced by generating deletions of 1-60 contiguous nucleotides that are linked to transgenes encoding a trait of interest, applicant’s marker allele having the sequence of SEQ ID NO: 61 which is a 4 base pair deletion linked to the DAS44406-6 transgene is obvious.
With respect to claim 2, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 1, see above.
Further, Cui as evidenced by Elsner teaches progeny plants, soybeans, seeds, and/or regenerable parts of the plants and seeds and progeny comprising soybean event pDAB8264.44.06.1 (DAS44406-6), as well as food or feed products made from any thereof (Cui, Column 4, Lines 10-14). As such Cui teaches processed (made) products (food or feed products) comprising the DNA molecule of Cui.
With respect to claim 3, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 2, see above.
With respect to claim 4, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 1, see above.
Further, Cui teaches DNA molecules comprising the pDAB8264.44.06.1 (DAS44406-6) transgenic event while Borchardt teaches creating marker alleles by introducing 1-60 contiguous nucleotide deletions linked to transgenes encoding herbicide tolerance, see analysis with respect to claim 1 above. Further, Cui explicitly teaches the DNA molecules comprising the transgenic event (Cui, Column 13, Lines 43-48).
With respect to claim 5, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 1, see above.
Further, Cui teaches “probes”, isolated nucleic acid molecules which are attached to a conventional detectable label or reporter molecule and which is complementary to a strand of genomic DNA from the soybean event of Cui (Cui, Column 21, Lines 47-54)
With respect to claim 6, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 5, see above.
With respect to claim 7, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 1, see above.
With respect to claim 8, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 7, see above.
With respect to claim 9, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 8, see above.
With respect to claim 10, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 9, see above.
With respect to claim 11, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 10, see above.
Further, Cui teaches a method of self-crossing the soybean plant and collecting seed thereof and selecting second progeny plants that demonstrate herbicide resistance (Cui, Column 13, Lines 5-21).
With respect to claim 12, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 10, see above.
Further, Cui teaches a method of the soybean plant comprising the transgene with another plant and selecting second progeny plants that demonstrate herbicide resistance (Cui, Column 13, Lines 5-11).
With respect to claim 13, Borchardt in view of Cui as evidenced by Elsner collectively teach all of the limitations of claim 1, see above.
Further, Cui teaches methods and assays for the detection of the pDAB8264.44.06.1 (DAS44406-6) transgenic event (Cui, Abstract).
As noted above in the obviousness analysis with respect to claim 1, it would have been obvious to modify the method of Borchardt to generate an artificial marker allele linked to the DAS44406-6 event of Cui as evidenced by Elsner because this would be applying a known technique to a known device ready for improvement to yield predictable results. Finally, it would have been obvious to modify the method of Cui to defat the soybean seed to produce defatted soybean seed meal, because this is an obvious use of soybean seed.
This rationale requires resolving the following Graham factual inquiries (MPEP 2143 D):
a finding that the prior art contained a “base” device (method, or product) upon which the claimed invention can be seen as an “improvement”;
a finding that the prior art contained a known technique that is applicable to the base device (method, or product);
a finding that one of ordinary skill in the art would have recognized that applying the known technique would have yielded predictable results and resulted in an improved system; and
whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness.
Addressing these inquiries one by one, Cui teaches a base device upon which the claimed invention can be seen as an “improvement”. Specifically Cui teaches soybeans containing the DAS44406-6. In fact the only distinction between the claimed invention and the soybeans of Cui is a 4 base pair deletion in the genomic soybean DNA flanking the transgene. Applicant made clear in the interview on 12/12/2025 and in the remarks dated 8/25/2025 that this deletion acts as a generic marker allowing sequences comprising this deletion to be identified, further Applicant stated that by itself this sequence has no function other than as a generic marker, see attached interview summary and the paragraph spanning pages 10-11 of Applicant’s Remarks dated 8/25/2025.
At the time of filing Borchardt taught a method of creating artificial marker alleles for traits of interest which include traits carried on transgenes and herbicide tolerance. These marker alleles can be created through the introduction of 1-60 base pair deletions in sequences linked to the trait of interest. Further Borchardt teaches that these methods are applicable to crop plants including soybean plants. Therefore, at the time of filing there was a finding that there was a known technique for creating artificial marker alleles linked to transgenes conferring traits of interest including herbicide tolerance. The base invention taught by Cui is a soybean plant comprising herbicide tolerance traits conferred by a transgene. Therefore the method of Borchardt is applicable to the base invention of Cui.
Third, at the time of filing a person having ordinary skill in the art would have recognized that applying the known technique of Borchardt to the transgenic soybean plants of Cui would have had the predictable result of producing a unique marker allele of the DAS44406-6 transgenic event that would allow for easy screening for this unique allele and correspondingly the transgenic event.
This would have had a predictable result because the techniques used in the method of Borchardt, specifically gene editing using the CRISPR/Cas system are well known in the art. These techniques are known for their applicability to a wide variety of organisms, accuracy, ease of use, and predictability in generating targeted modifications to a sequence. Given that the target sequence was taught by Cui and known in the art at the time of filing and that the unique marker alleles of Borchardt can be introduced using the CRISPR/Cas system, at the time of filing, the ordinary artisan would have recognized that applying the known technique would have yielded predictable results and resulted in an improved transgenic soybean plant.
Given, that applicant’s invention is a generic marker allele and that the combined teachings of Borchardt in view of Cui as evidenced by Elsner teach soybean plants having unique marker alleles linked to transgenes that are produced by generating deletions of 1-60 contiguous nucleotides that are linked to transgenes encoding a trait of interest, applicant’s marker allele having the sequence of SEQ ID NO: 61 which is a 4 base pair deletion linked to the DAS44406-6 transgene is obvious.
As such claims 2-13 are rejected as obvious under Borchardt in view of Cui as evidenced by Elsner.
Conclusion
All claims are rejected.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached on 7:30 to 5:00.
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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.
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/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663