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 the Claims
The arguments filed 18May2026 are acknowledged and have been fully considered. No claims are amended: claims 56-71 remain pending, were previously presented, and examined on the merits herein. Claims 1-55 and 72 were previously canceled.
No Rejections are Withdrawn
For the sake of a clear record, Applicant’s reply filed 18May2026 does not overcome any of the rejections of record.
Anyone reviewing this file history may wish to review the outstanding rejections alongside the Examiner’s proposed claim amendments at pages 20-21 of the nonfinal action dated 18November2025 because the proposed claims may clarify the basis upon which the rejections are made and maintained. Explanatory comments were provided by the Examiner (accompanying the Interview Summary of record 18November2025)—those comments are labeled as Office Action Appendix documents (2 separate files) dated 18November2025 (doc code “OA.APPENDIX”). The explanations are within comment boxes on the proposed claims emailed to Applicant.
Claim Interpretation & File History
[Copied from the Final Action Dated 28March2025 → ] Applicant describes SEQ ID NO: 2 as a Yr5 amino acid sequence1, SEQ ID NO: 3 as a Yr7 amino acid sequence2, and SEQ ID NO: 6 as a YrSP amino acid sequence3.
[Copied from the Final Action Dated 28March2025 → ] Please note that the “ZHANG thesis” discussed throughout the file history is not prior art. Also, the “ZHANG thesis” author (ZHANG, Jianping) is a named inventor of this application.
[Copied from the Final Action Dated 28March2025, See the Response to Applicant’s Remarks section for new content → ] Please note that the “introducing a nucleic acid” language within these claims does not encompass plant breeding/introgression via crosses or gene editing (e.g., using nucleases such as CRISPR/Cas techniques)—through Applicant’s claim amendments and arguments of record, these claims are limited to “introducing” via transgenic techniques. This is important to know because otherwise it may appear as though (1) anticipation or obviousness rejection(s) are missing and/or (2) the Written Description and Enablement rejections herein have not addressed gene editing. Neither (1) or (2) are needed herein because the claims are now limited to transgenic techniques.
RE plant breeding/introgression via crosses: please note the claim amendments and arguments filed 27December2024 (part (a) of claim 28) then the final office action dated 27January2023 wherein the Office withdrew an anticipation rejection over FENG et al. (who teach certain plant breeding methods and plants with increased obtained thereby) because the claims were amended to remove plant breeding/introgression via crosses from the claimed scope (see Applicant’s arguments filed 27December2024).
RE gene editing: part (b) of claim 28 (first introduced 27December2024) was explicitly directed toward modification via gene editing (e.g., using nucleases such as via CRISPR/Cas techniques). Reference to “mutating or editing genomic material” is now removed from the pending and examined claims. Therefore, “introducing a nucleic acid” via gene editing is removed from the pending and examined claims.
If Applicant disagrees with these interpretations, an appropriate response should be made of record to that effect. Applicant is reminded that “the doctrine of prosecution disclaimer ensures that claims are not construed one way [by Applicant] in order to obtain their allowance and in a different way against accused infringers” (SandBox Logistics LLC v. Proppant Express Invs. LLC, 813 F. App'x 548, at 556 (Fed. Cir. 2020)) and, to that end, “[Applicant' s] failure to challenge the Examiner' s understanding amounts to a disclaimer” (SandBox v. Proppant infra at 554; citing Biogen Idec, Inc. v. GlaxoSmithKline LLC, 713 F.3d 1090, at 1096 (Fed. Cir. 2013)).
Furthermore, Applicant is reminded of their “Duty of Disclosure, Candor, and Good Faith” (see 37 C.F.R. § 1.56 and MPEP § 2001).
Response to Applicant’s Remarks 18May2026:
(1) Applicant’s Remarks 18May2026 (hereinafter “Remarks”) MAINTAIN the argument that these claims encompass introducing Yr5, Yr7, or YrSP by gene editing (Remarks at pages 5-10).
This REMAINS unpersuasive for the reasons of record (see the nonfinal action 18November2025 at pages 3-4). Also, Applicants Remarks at page 9 seem to agree with the Examiner’s interpretation: Applicant is explaining that pending claim 56 (to which all other pending claims refer) is limited to (what was) part (a) of now-canceled claim 28 (i.e., directed toward transformation). As explained within the Applicant’s Remarks, part (b) of now-canceled claim 28 was directed toward “mutating or editing genomic material” and now part (b) “mutating or editing genomic material” is not encompassed by the pending and examined claims. Applicant then asserts that they are not estopped from claiming “editing genomic material” here, which is where the Applicant and Examiner disagree. The Examiner maintains that Applicant cannot recapture “editing genomic material” here (i.e., in this application) because of estoppel. The Examiner wonders whether Applicant is trying to rescind a narrowing amendment or argument (such as in advance of a continuation application being filed with claims directed toward “editing genomic material”)? If yes, please make the record clear here and/or in the documents accompanying one such continuation application filing (see Hakim v. Cannon Avent Group, PLC, 479 F.3d 1313, 1317-18 (Fed. Cir. 2007) and associated “Hakim statement” or “Recapture statement” guidance). Genome editing has been removed from this application, but Applicant may consider filing a continuation application to pursue “editing genomic material” (via CRISPR, for example).
The Remarks provide the following (pages 9-10):
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(2) Applicant argues that the claims are to be given their broadest reasonable interpretation during examination and that, in any event, the courts interpret claims (not the Examiner) (Remarks at pages 6-7).
The Remarks provide the following (page 7):
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This is not persuasive because, as evidenced by the Written Description and Enablement rejections of record and herein (as well as the corresponding “Response to Applicant’s Remarks” sections), the Examiner is already giving these claims their broadest reasonable interpretation. Please note that the Examiner has considered the explicit language of the claims in view of the specification and prior art (note citations throughout the Written Description and Enablement rejections, for example). Applicant’s comment regarding courts interpreting claims is also understood to mean that courts interpret patented/issued claims (see the language quoted by Applicant at Remarks page 7 regarding “patented claims”) and that the interpretation standard is different before issuance (broadest reasonable interpretation) versus after issuance (Phillips standard). Applicant’s position is consistent with the Examiner’s understanding, but since these claims are not yet issued, it is unclear how Applicant’s comments about court interpretation (under the Phillips standard) are relevant.
(3) Applicant asserts that the Examiner’s claim interpretation is perhaps based on Examiner’s misunderstanding of the claims (that gene editing, by CRISPR for example, was always encompassed by the claims) (Remarks at the bottom of page 7-8).
The Remarks provide the following (top of page 8):
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As an initial matter and for the ease of anyone reviewing this file history, please note that the law firm representing Applicant has changed during the examination of this application and that the assigned Examiner has changed during the examination of this application. The first office action by this Examiner was the first action on the merits (the nonfinal action dated 27July2022, the only preceding action having been a Restriction Requirement by the former Examiner of record). The nonfinal action dated 27July2022 provides evidence to show that this Examiner understood genomic editing (e.g., via CRISPR) to be reasonably encompassed by the then-pending-claims. For example, the Written Description rejection by this Examiner at page 2, lines 13-16 explicitly acknowledges gene editing by CRISPR technology:
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As shown by the nonfinal action dated 27July2022 and the screenshot above, Applicant’s assertion is not persuasive. For anyone reviewing this file history, the Examiner believes that the claims were amended during the course of examination to remove the “editing genomic material” CRISPR concept (e.g., what was part (b) of claim 28) and that, now, the Applicant is not happy with having done so. As said of record, (RE gene editing) previous claim amendments deleted “editing genomic material” from the claims and (RE crosses/breeding) a prior art rejection over FENG et al. was previously withdrawn because these claims were amended and argued to not encompass plant crosses/breeding. Taken together, this is why the Examiner believes that these claims are directed toward transgenic techniques (not gene editing via CRISPR or crosses/breeding) and why the Examiner believes that Applicant is estopped from reintroducing that subject matter into this application (the Examiner believes that gene editing via CRISPR or crosses/breeding methods may be pursued in a continuation application). Applicant does not agree with the Examiner (as evidenced by their many Remarks on the subject).
Claim Rejections - 35 USC § 112(b) or second paragraph - 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.
Claim 56 (and, therefore, claims 57-71 which refer thereto without correcting the issue) REMAIN 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.
Claim 56 says that a Yr5 sequence (SEQ ID NO: 2), Yr7 sequence (SEQ ID NO: 3), and/or YrSP sequence (SEQ ID NO: 6) is introduced into the [parental] wheat plant’s genome “at a locus different from a native locus of a Yr5, Yr7, or YrSP wheat yellow rust resistance gene”. It is not clear from this language whether the parental wheat plant already comprises the Yr5/Yr7/YrSP gene(s) or not.
To ensure a clear record, this rejection is based on the fact that the genetics of the parent plant are not defined and the parent plant does not need to comprise any of Yr5, Yr7, or YrSP. Because of the breadth of parent plants in these claims, what constitutes a “native locus” is indefinite. This is material because “native locus” is being defined with respect to a location within a parent plant’s chromosome—but the parent plants of these claims need not comprise any of Yr5, Yr7, or YrSP; so how is someone supposed to determine where the “native locus” is?
Response to Applicant’s Remarks 18May2026:
(1) Applicant asserts that a person with ordinary skill in the art (a “POSA”) would know where the native locus of Yr5, Yr7, and YrSP is (Remarks at page 11) and, therefore, these claims are definite.
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This is not persuasive because Applicant continues to overlook the basis for this rejection. As said of record, “this rejection is based on the fact that the genetics of the parent plant are not defined and the parent plant does not need to comprise any of Yr5, Yr7, or YrSP.” The fact that the “parental wheat plant” may have any underlying genetic profile means that the “native locus” concept is indefinite. The specification does not provide a limiting definition of what a “native locus” is, so it is given its Broadest Reasonable Interpretation consistent with what a person with ordinary skill in the art would understand “native locus” to mean. The resulting interpretation of “native locus” is consistent with what was said within the LAGUDAH Declaration2, notably that it is a location concept. Please note that by way of the LAGUDAH Declaration2, Applicant is urging that the “native locus” is defined by both location and content (namely, the location that comprises a particular gene). Applicant continues to assert that the location which is the “native locus” is that which comprises a particular gene (i.e., someone would have to know the location of a gene before they can determine that the location is the “native locus” within these claims). Page 2, ¶9 of the LAGUDAH Declaration2 states the following:
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To help understand the issue, please imagine that someone just hands you a wheat plant (we know nothing about its parentage, resistance traits, etc.)—per Applicant (and the LAGUDAH Declaration2), we would identify the “native locus” therein by looking for the Yr5, Yr7, or YrSP gene sequence therein. If the wheat plant we have been handed does not comprise the Yr5, Yr7, or YrSP gene that we are looking for; then we cannot identify the “native locus” because the “native locus” is supposed to be the location “that harbors” the Yr5, Yr7, or YrSP gene. Applicant’s description of what “native locus” means per the LAGUDAH Declaration2 only works if the “parental wheat plant” already comprises the Yr5, Yr7, or YrSP gene being introduced into it (i.e. a gene stacking scenario where the resulting plant comprises at least two copies of the Yr5, Yr7, or YrSP gene) and the Examiner maintains that Applicant does not intend for the “parental wheat plants” of these claims to be so limited (i.e., it remains clear that these claims are intended to encompass introducing Yr5, for example, into a wheat plant that does not already comprise Yr5). ← This is why the Examiner continues to suggest that the claims recite the location itself (“nuclear 2BL chromosome”) instead of the “native locus” concept, because reciting the location itself eliminates the problem of working with a “parental wheat plant” that does not already comprise the Yr5, Yr7, or YrSP gene being introduced. Here again, Applicant is encouraged to thoughtfully review the Examiner’s proposed claim amendments which would be remedial of this rejection (note the highlighted portion of proposed claim 73, for example):
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(2) Applicant continues to assert that the Examiner does not understand “locus” and “gene” concepts (Remarks at page 12):
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This remains unpersuasive as evidenced by the record, within which the Examiner demonstrates the requisite understanding of these concepts (e.g., this indefiniteness rejection has and continues to say “… “native locus” is being defined with respect to a location within a parent plant’s chromosome ….”). Also, as evidenced by the discussion of the LAGUDAH Declaration2 document throughout the “Response to Applicant’s Remarks” sections in both the nonfinal action dated 18November2026 and here, the LAGUDAH Declaration2 remains acknowledged by the Examiner and has been fully considered—its contents do not overcome the rejections herein.
Claim Rejections - 35 USC § 112(a) or first paragraph – Written Description & Enablement
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.
WRITTEN DESCRIPTION:
Claims 56-71 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.
↓ Rejection Copied from the Nonfinal Dated 18November2025, Please See Response to Remarks ↓
Executive Summary of the Issues (parts a-c having been withdrawn previously):
(d) claims 56-71 are directed toward modifying a plant via transformation techniques to introduce any one of, or any combination of, Yr5 (SEQ ID NO: 2), Yr7 (SEQ ID NO: 3), YrSP (SEQ ID NO: 6) under the control of any regulatory element(s) into any parental wheat plant (i.e., a wheat plant having any genomic composition including the presence of Yellow Rust (Yr) resistance gene(s)) to enhance resistance to any Puccinia striiformisi f. sp. Tritici (PST) race as compared to that of the parental/untransformed wheat plant.
These claims remain rejected because of (1) the breadth of gene combinations that may be introduced into the wheat plant and, according to these claims, enhance resistance to at least one PST race (e.g., these claims encompass introducing just Yr7, or just YrSP, or Yr7 and YrSP, etc.). Also because of (2) the breadth of regulatory elements which may be used to express the Yr5, Yr7, or YrSP gene (e.g., constitutive, tissue-specific, and developmentally-specific promoters, etc., may all be used in these plants/parts or to practice these methods). Also because of (3) the breadth of “parent plants” (see indefiniteness issue hereinabove) in these claims and supposedly increasing/enhancing resistance to any PST race as compared to the parent plant. Finally, because (4) the plants in these claims purportedly have increased/enhanced resistance to PST in general whereas it is recognized in the art (and, indeed, the specification4) that resistance is isolate/race-specific in this context Yr7 and YrSP no longer provide resistance to certain PST isolates/races whereas Yr5 does). It is perhaps helpful to note that, as said in the specification at the paragraph bridging pages 1-2, because Yr7 and YrSP are no longer effective in the field for PST resistance, a skilled artisan would not recognize introducing just Yr7, or just YrSP, or Yr7 and YrSP into a wheat plant as an effective means for increasing/enhancing PST resistance (of any isolate/race) and, yet, that remains encompassed by these claims.
Please see the claim amendments proposed by the Examiner (attached to this action including explanatory comments and copied below without comments) for further clarification as to why these claims remain rejected here and how these issues may be remedied.
Rejection (Largely Copied from Final Dated 28March2025):
The specification only describes the use of prior art plant breeding, diagnostic marker, and sequence techniques to obtain the polynucleotide and polypeptide sequences of the yellow rust resistance genes/proteins YrSP, Yr5, and Yr7 from a specific type of hexaploid wheat: Triticum aestivum.5 To be sure, the plant breeding steps of the specification6 are believed to have made Triticum aestivum plants having a conferred or enhanced resistance to certain Puccinia Striiformisi f. sp. tritici (PST) strains because those steps would have introduced at least one of YrSP, Yr5, and Yr7 into the resulting F1 and F2 plants7. The specification only describes YrSP, Yr5, and Yr7 as being relevant to the specific yellow (stripe) rust fungal pathogen Puccinia Striiformisi f. sp. tritici (PST)8 and, indeed, the specification is believed to only describe conferring or enhancing the resistance of the hexaploidy wheat plant T. aestivum to certain PST strains through the use of plant breeding to make certain F1 and F2 plants.9 For clarity of the record, the prior art was well aware of the relationship between YrSP, Yr5, and Yr7 to PST resistance in wheat (including T. aestivum).10
To ensure clarity, the specification does not describe even one incidence of either transformation or genome editing—it follows that the specification, therefore, does not describe conferring a wheat plant’s resistance to yellow (stripe) rust fungus via transformation or genome editing using the NLR polypeptides being claimed.
As an initial matter (and for the sake of a clear record) “increasing resistance” was previously recited, then removed, from the claims. The claims currently pending and under examination now recite “enhanced resistance”. These claims still encompass transforming a wheat plant/cell with at least one of Yr5, Yr7, and YrSP when the plant already comprises at least one of Yr5, Yr7, and/or YrSP (the claims do not specify either the genetic background of the parental wheat plant/cell being transformed nor the specific combination of genes being transformed thereinto to achieve the claimed “enhanced” resistance to PST). As evidenced by, for example, ZHENG et al. at Fig. 4 on page 12 (top row, left side) it was known in the prior art that different Yr genes (including different combinations of Yr genes) will have a disparate impact on stripe rust resistance in wheat.11 As shown by ZHENG et al., simply introducing Yr5 into a wheat plant/cell, for example, is not enough information for a skilled artisan to reasonably expect “enhancing” resistance to any particular yellow (stripe) rust fungus because (as evidenced by ZHENG et al.) such a person would know that the wheat’s existing genetic background is material for “conferring” or “enhancing” such resistance (e.g., does the wheat plant/cell already comprise other Yr genes such as Yr6, Yr29, Yr30, Yr33, and/or Yr41? Based on at least Fig. 4 of ZHENG et al., a skilled artisan would need to know that information in order to reasonably expect “conferring” or “enhancing” any resistance via the introduction of Yr5 thereinto).
These claims also continue to encompass transformation with any type or combination of regulatory sequences (e.g., any constitutive or tissue-specific promoter) to deliver, incorporate, and express Yr5, Yr7, and/or YrSP in a [parental] wheat plant/cell to confer or enhance PST resistance onto that wheat plant/cell. The specification does not specifically describe even one transformation of a plant or cell so as to express an NLR polypeptide (e.g., transformation with any of a Yr5, Yr7, or YrSP sequence). It follows that the specification also does not specifically describe the transformation materials (such as vector composition) to conduct one such transformation. Therefore, the specification does not show that Applicant (at the time this application was filed) was in possession of conferring or enhancing the PST resistance of a wheat plant/cell. The prior art does not appear to correct these deficiencies.
To be clear, general transformation of wheat plants (including T. aestivum), while more difficult than certain other crop plants, has been done by the prior art.12 But like the present specification, there is no evidence showing that the prior art had described the transformation of a wheat plant/cell (even hexaploid wheat T. aestivum) to express an NLR polypeptide (e.g., a yellow (stripe) rust resistance gene like YrSP, Yr5, Yr7, or a combination thereof). It follows that there is no evidence showing that the prior art had conferred or enhanced PST resistance onto a transformed wheat plant/cell by introducing and expressing therein an NLR polypeptide (e.g., by transformation with any of a Yr5, Yr7, or YrSP sequence). To be clear, the prior art does not supplement this specification by providing further guidance as to what materials (e.g., promoters) would be necessary and sufficient for successful expression of an NLR polypeptide to confer or enhance PST resistance to a wheat plant or cell (e.g., is constitutive expression going to work to achieve the claimed phenotype? Or perhaps tissue-specific expression is needed to obtain the claimed phenotype? Perhaps overexpression of Yr5, Yr7, or YrSP is deleterious to the plant unless the plant is already under pathogen-induced stress meaning that a stress-induced promoter is needed to obtain the claimed phenotype?).
Furthermore, it was well known in the prior art that simply identifying a gene (or genes) that are associated with a particular phenotypic effect does not mean that useful application of that gene (or genes) in transformation techniques is straight forward. At the very least, it was well understood that the effect of a transgene(s) on a plant phenotype is highly dependent upon the expression cassette (meaning that it must be understood what promoters can be used to impact phenotype (i.e., expression levels, time, location, and/or duration of the transgene must be understood)).13 If the transgene(s) is endogenous to the transgenic plant, expression (or suppression) of the endogenous gene’s expression must also be understood and accounted for.14 Finally, it was well understood that the transgene’s insertion location is material to whether or not the transgene achieves useful expression for impacting phenotype.15 These facts are exemplified in prior publications by the inventor(s): albeit with a different class of proteins, LAGUDAH et al.16 demonstrate via negative/”S” susceptible results at Table 6 (page 71) that at least the particulars of an expression cassette must be described with particularity (e.g., promoters and terminators) in order to reliably impact phenotype via transformation techniques.
As said above, the specification does not describe even one incidence of transformation to achieve the claimed phenotype effect. Further, the specification does not specifically describe the materials necessary for doing that (e.g., expression vector components including promoter(s) and terminator(s)). Therefore, the specification does not disclose the complete structure (or acts of the process) of the claimed invention as a whole and neither the specification nor the prior art disclose other relevant “identifying characteristics” sufficient to describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan at the time of filing would reasonably recognize Applicant(s) was in possession of the full metes and bounds of the claimed invention.17 The specification, in view of the prior art, merely provides ‘a result that one might achieve if one made that invention’, which is not sufficient to satisfy the written description requirement.18
Response to Applicant’s Remarks 18May2026:
(1) Applicant asserts that the specification, as further explained by LAGUDAH Declaration2, sufficiently describes the full metes and bounds of these claims and that knowledge of an isolated resistance gene is, itself, enough for Written Description (pages 13-14 of the Remarks):
Page 13 of the Remarks states:
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This is not persuasive. As an initial matter, the Examiner continues to disagree that the specification (when read in view of the prior art) evidences possession of the full metes and bounds of these claims. Further, Applicant’s argument that knowledge of a resistance gene structure/sequence, alone, is enough for possession of a method of using one such resistance gene to generate a plant with enhanced resistance directly contradicts Applicant’s own results in LAGUDAH et al.19 (demonstrating negative/”S” susceptible results at Table 6 (page 71) after having introduced a resistance gene thereinto). As evidenced by Applicant’s own LAGUDAH et al., knowledge of a resistance gene’s structure/sequence is not enough, by itself, for possession of method of using one such resistance gene to generate a plant having enhanced resistance—something about expression must be understood before an impact on resistance may be reasonably expected. As said of record, the effect of a transgene(s) on a plant phenotype is highly dependent upon the expression cassette (meaning that it must be understood what promoters can be used to impact phenotype (i.e., expression levels, time, location, and/or duration of the transgene must be understood)).
(2) Applicant asserts that the Examiner is not (has not) given “proper deference” to the LAGUDAH Declaration2 (Remarks at page 14).
Page 14 of the Remarks states:
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This is not persuasive. As evidenced by the discussion of the LAGUDAH Declaration2 document throughout the “Response to Applicant’s Remarks” sections in both the nonfinal action dated 18November2026 and here, the LAGUDAH Declaration2 remains acknowledged by the Examiner and has been fully considered, it is also maintained that its contents do not overcome the rejections herein.
SCOPE OF ENABLEMENT:
Claims 56-71 REMAIN under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for modifying a hexaploidy Triticum aestivum plant via plant breeding techniques so that the plant comprises and expresses a heterologous YrSP, Yr5, and/or Yr7 protein and therefore has a conferred resistance to certain Puccinia Striiformisi f. sp. tritici (PST) isolates/races, does not reasonably provide enablement for (d) the use of transformation (or gene editing) techniques to achieve the claimed functional result. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make the invention commensurate in scope with these claims without undue trial and error experimentation.
↓ Rejection Copied from the Nonfinal Dated 18November2025, Please See Response to Remarks ↓
The factors used (and weighed) to determine whether a specification satisfies the enablement requirement (and, thus, whether any necessary experimentation would be ‘undue’) include, but are not limited to, the following: (A) the breadth of the claims; (B) the nature of the invention; (C) the state of the prior art; (D) the level of one of ordinary skill; (E) the level of predictability in the art (“if one skilled in the art can readily anticipate the effect of a change within the subject matter to which the claimed invention pertains, then there is predictability in the art”20); (F) the amount of direction provided by the specification; (G) the existence of working or prophetic examples; and (H) the quantity of experimentation needed to make or use the invention based on the content of the specification read in view of the prior art (including whether “one would expect to be able to extrapolate [the example(s)] across the entire scope of the claims”21).22
Regarding (A) the breadth of the claims (where (d) here tracks that of the Written Description rejection above):
(d) claims 56-71 are directed toward modifying a plant via transformation techniques to introduce any one of, or any combination of, Yr5 (SEQ ID NO: 2), Yr7 (SEQ ID NO: 3), YrSP (SEQ ID NO: 6) under the control of any regulatory element(s) into any parental wheat plant (i.e., a wheat plant having any genomic composition including the presence of Yellow Rust (Yr) resistance gene(s)) to enhance resistance to any Puccinia striiformisi f. sp. Tritici (PST) race as compared to that of the parental/untransformed wheat plant. These claims remain rejected because of (1) the breadth of gene combinations that may be introduced into the wheat plant and, according to these claims, enhance resistance to at least one PST race (e.g., these claims encompass introducing just Yr7, or just YrSP, or Yr7 and YrSP, etc.). Also because of (2) the breadth of regulatory elements which may be used to express the Yr5, Yr7, or YrSP gene (e.g., constitutive, tissue-specific, and developmentally-specific promoters, etc., may all be used in these plants/parts or to practice these methods). Also because of (3) the breadth of “parent plants” (see indefiniteness issue hereinabove) in these claims and supposedly increasing/enhancing resistance to any PST race as compared to the parent plant. Finally, because (4) the plants in these claims purportedly have increased/enhanced resistance to PST in general whereas it is recognized in the art (and, indeed, the specification23) that resistance is isolate/race-specific in this context Yr7 and YrSP no longer provide resistance to certain PST isolates/races whereas Yr5 does). It is perhaps helpful to note that, as said in the specification at the paragraph bridging pages 1-2, because Yr7 and YrSP are no longer effective in the field for PST resistance, a skilled artisan would not recognize introducing just Yr7, or just YrSP, or Yr7 and YrSP into a wheat plant as an effective means for increasing/enhancing PST resistance (of any isolate/race) and, yet, that remains encompassed by these claims. Please see the claim amendments proposed by the Examiner (attached to this action including explanatory comments and copied below without comments) for further clarification as to why these claims remain rejected here and how these issues may be remedied.
The claims continue to encompass a broad scope of subject matter.
↓ What Follows is Largely Copied from Final Dated 28March2025, Please See Response to Remarks ↓ Section for New Content
Regarding (B) the nature of the invention, (F) the amount of direction provided by the specification; and (G) the existence of working or prophetic examples:
The specification teaches the use of prior art plant breeding, diagnostic marker, and sequencing techniques to obtain the polynucleotide and polypeptide sequences of the yellow (stripe) rust resistance genes/proteins YrSP, Yr5, and Yr7 from a specific type of hexaploid wheat: Triticum aestivum.24 The plant breeding steps of the specification25 are believed to have made Triticum aestivum plants having a conferred or enhanced resistance to certain Puccinia Striiformisi f. sp. tritici (PST) strains because those steps would have introduced at least one of YrSP, Yr5, and Yr7 into the resulting F1 and F2 plants.26 The specification does not teach conferring or enhancing PST resistance using transgenic techniques (e.g., introducing and expressing one or more of YrSP, Yr5, and/or Yr7 within a plant).
The amount of direction provided by the specification (including examples) is very narrow compared to the full breadth of the claims.
Regarding (C) the state of the prior art; (D) the level of one of ordinary skill; and (E) the level of predictability in the art:
The prior art teachings are commensurate in scope with the teachings of this specification.27 Therefore, the teachings of the prior art do not compensate for the lack of teachings by the specification.
Furthermore, it was well known in the prior art that simply identifying a gene (or genes) that are associated with a particular phenotypic effect does not mean that useful application of that gene (or genes) in transformation techniques is straight forward. At the very least, it was well understood that the effect of a transgene(s) on a plant phenotype is highly dependent upon the expression cassette (meaning that it must be understood what promoters can be used to impact phenotype (i.e., expression levels, time, location, and/or duration of the transgene must be understood)).28 If the transgene(s) is endogenous to the transgenic plant, expression (or suppression) of the endogenous gene’s expression must also be understood and accounted for.29 Finally, it was well understood that the transgene’s insertion location is material to whether or not the transgene achieves useful expression for impacting phenotype.30 These facts are exemplified in prior publications by the inventor(s): albeit with a different class of proteins, LAGUDAH et al.31 demonstrate via negative/”S” susceptible results at Table 6 (page 71) that at least the particulars of an expression cassette must be described with particularity (e.g., promoters and terminators) in order to reliably impact phenotype via transformation techniques.
Regarding (H) the quantity of experimentation needed to make or use the invention based on the content of the specification read in view of the prior art:
Because the claims encompass conferring resistance using any one of Yr5, Yr7, or YrSP genes as well as any combination thereof (noting that, as confirmed by the specification, Yr7 and YrSP are no longer useful for conferring broad PST resistance32), and breadth of techniques for modifying a plant’s genomic material; and because the specification and the prior art only teach plant breeding methods in specific wheat plants (e.g., hexaploidy T. aestivum) using specific NLR genes/polypeptides (T. aestivum YrSP, Yr5, and/or Yr7) located on the long arm of chromosome 2 (referred to as “2BL” in the art)33 to confer or enhance resistance to a specific fungal pathogen (PST), a skilled artisan would not expect to be able to extrapolate the limited teachings in the specification and prior art across the entire scope of the claims. A skilled artisan could not follow the guidance presented within the specification or prior art to practice the claimed method without first engaging in undue trial and error experimentation such as by having to design transformation protocols using (i) a variety of [parental] wheat plants (i.e., selecting plants with a variety of genomic compositions); (ii) testing the insertion of Yr5, Yr7, YrSP, or any combination thereof into the various [parental] wheat plant varieties; (iii) testing a variety of regulatory elements for Yr5/Yr7/YrSP expression (e.g., using a constitutive promoter or tissue-specific promoter and perhaps having to use a different promoter for each of the different genes); and then assaying for whether “enhanced” PST resistance is achieved (as compared to the parental wheat plant). If “enhanced” PST resistance is not achieved, then any one or more of (i), (ii), and (iii) would need to be redesigned and assayed until “enhanced” PST resistance is achieved. This amount of experimentation is not merely quantitative and is certainly not routine34—in fact, these hypothetical experiments are the type that often result in a substantial inventive contribution (i.e., conception). For at least these reasons, the specification does not enable the full scope of the claimed subject matter.
Response to Applicant’s Remarks 18May2026:
(1) As was argued for the above Written Description rejection, Applicant asserts that knowledge of a resistance gene’s structure/sequence alone is sufficient to enable its use in producing a plant having an enhanced resistance (Remarks at page 15).
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This is not persuasive (for Written Description or Enablement) as supported by Applicant’s own LAGUDAH et al.35 (demonstrating that simply introducing a resistance gene into a plant, alone, is not sufficient to cause enhanced resistance (page 71 regarding the results as summarized in Table 6)). The difference here, as compared to the Written Description analysis, is whether it would have been undue experimentation for a skilled artisan at the time this application was filed to make and/or use the claimed subject matter. In view of LAGUDAH et al.36 , the specification and other prior art; it is not persuasive to say that a gene structure/sequence alone is sufficient to show enablement (i.e., to overcome this enablement rejection). It is maintained, as evidenced by Applicant’s own LAGUDAH et al.37, that something about expression must be understood before an impact on resistance may be reasonably expected: the effect of a transgene(s) on a plant phenotype is highly dependent upon the expression cassette (meaning that it must be understood what promoters can be used to impact phenotype (i.e., expression levels, time, location, and/or duration of the transgene must be understood)). Applicant is encouraged to review the Examiner’s proposed claims at pages 20-21 of the nonfinal action 18November2026 (copied herein below as well) for claims which the Examiner believes would be enabled.
(2) Applicant summarizes what they believe a skilled artisan at the time this application was filed would have known (Remarks at page 16) and state that the LAGUDAH Declarations 1&2 both show that the Applicant has “successfully implemented the claimed invention without undue burden as evidenced following the methods in Ishida et al. (2015).” (Remarks at the bridge of pages 16-17, copied below).
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These pages of argument are acknowledged, but they are not sufficient to overcome this rejection. The enablement analysis looks toward the specification and prior art together and asks whether they teach other skilled artisans how to make and use the claimed subject matter without undue trial and error experimentation: the Applicant successfully practicing one embodiment (using Yr5 and YrSP in Fielder wheat, which does not comprise Yr5, Yr7, or YrSP) within the broadly claimed subject matter and after the effective filing date (post-filing ZHANG thesis, see also ¶¶42-44 on page 9 of the LAGUDAH Declaration2 copied below) does not enable others to make and use the full scope of what is being claimed.
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For a specific recommendation to overcome these Enablement issues, see Examiner’s proposed claim amendments at pages 20-21 of the nonfinal 18November2025 (also copied herein below).
(3) Applicant asserts that the Examiner is not (has not) given “proper deference” to the LAGUDAH Declaration2 (Remarks at page 17).
This is not persuasive. As evidenced by the discussion of the LAGUDAH Declaration2 document throughout the “Response to Applicant’s Remarks” sections in both the nonfinal action dated 18November2026 and here, the LAGUDAH Declaration2 remains acknowledged by the Examiner and has been fully considered, it is also maintained that its contents do not overcome the rejections herein.
(4) Applicant acknowledges that PST resistance is race-specific and asserts that a skilled artisan would not have interpreted the claims as requiring enhanced resistance to all PST races (Remarks at page 18). Applicant asserts that the Examiner is “once again” misinterpreting the claims.
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This is not persuasive. Applicant should please focus their attention on what resistance genes, if any, the “parental wheat plant” of claim 56 has before transformation and which of (or which combination of) Yr5, Yr7, and YrSP are introduced into the “parental wheat plant”. In having done so, it is believed that the relevance of PST race will become clear (as discussed of record, because Yr7 and YrSP are no longer useful for conferring broad PST resistance (per the art and this specification38), it is unreasonable to suggest that introducing Yr7 or YrSP into a “parental wheat plant” will enhance PST resistance and, yet, the claims continue to encompass this scenario). If Applicant remains unclear about the basis upon which this rejection is made and maintained, they should call the Examiner.
Conclusion
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.
Please see the Interview Summary of record 18November2025 regarding claim amendments which were proposed by the Examiner to move this case forward (and which were rejected by Applicant)—in response to Examiner’s proposal, Applicant requested the nonfinal action via telephone on 31October2025. For ease of review, the proposed claim amendments are copied below (but the accompanying explanatory comments are not, please see the Office Action Appendix documents (2 separate files) dated 18November2025 (doc code “OA.APPENDIX”) for those comments which are directly on the proposed claim amendments as comment boxes).
These are the PROPOSED Claim Amendments submitted by the Examiner to Applicant (were rejected):
1.-72. (Canceled)
73. (New) A method of producing a modified Triticum plant, plant part, or cell having increased resistance to Puccinia striiformis f. sp. Tritici (“PST”), comprising:
(a) introducing a recombinant nucleic acid molecule into the nuclear genome of a Triticum plant, plant part, or cell (“unmodified Triticum plant, plant part, or cell”) and
(b) selecting a Triticum plant, plant part, or cell from (a) for comprising the recombinant nucleic acid molecule and for having increased resistance to at least one PST race as compared to the unmodified Triticum plant, plant part, or cell,
thereby producing a modified Triticum plant, plant part, or cell;
wherein the recombinant nucleic acid molecule comprises a Yr5 polynucleotide sequence under the control of a Yr5 promoter and that encodes the amino acid sequence of SEQ ID NO: 2,
wherein the unmodified Triticum plant, plant part, or cell does not comprise a Yr5 polynucleotide sequence on its nuclear 2BL chromosome; and
wherein the modified Triticum plant, plant part, cell, does not comprise the recombinant nucleic acid molecule on its nuclear 2BL chromosome.
74. (New) The method of claim 73, further comprising:
(c) obtaining a modified Triticum plant from the modified Triticum plant part or cell of (b), wherein the modified Triticum plant comprises the recombinant nucleic acid molecule and has increased resistance to at least one PST race as compared to the unmodified Triticum plant, plant part, or cell.
75. (New) The method of claim 74, further comprising:
(d) obtaining a progeny plant, plant part, or cell from the modified Triticum plant, plant part, or cell of (b), or from the modified Triticum plant of (c), wherein the progeny plant, plant part, or cell comprises the recombinant nucleic acid molecule and has increased resistance to at least one PST race as compared to the unmodified Triticum plant, plant part, or cell.
76. (New) The method of claim 73, wherein the Yr5 polynucleotide sequence comprises the sequence of SEQ ID NO: 4.
77. (New) The method of claim 73, wherein the recombinant nucleic acid molecule further comprises:
(1) a Yr7 polynucleotide sequence under the control of a Yr7 promoter and that encodes the amino acid sequence of SEQ ID NO: 3 and/or
(2) a YrSP polynucleotide sequence under the control of a YrSP promoter and that encodes the amino acid sequence of SEQ ID NO: 6.
78. (New) The method of claim 77, wherein
(1) the Yr7 polynucleotide sequence comprises the sequence of SEQ ID NO: 5 and/or
(2) the YrSP polynucleotide sequence comprises the sequence of SEQ ID NO: 7.
79. (New) The method of claim 73, wherein the modified Triticum plant, plant part, or cell is of the species Triticum aestivum.
80. (New) The method of claim 73, wherein the modified Triticum plant, plant part, or cell is of the species Triticum turgidum.
81. (New) The method of claim 73, wherein the modified Triticum plant part is a seed.
82. (New) The method of claim 81, further comprising:
(c) planting the seed and growing a modified Triticum plant therefrom, wherein the modified Triticum plant comprises the recombinant nucleic acid molecule and has increased resistance to at least one PST race as compared to the unmodified Triticum plant, plant part, or cell.
83. (New) The method of claim 75, wherein the progeny plant part is a seed.
84. (New) The method of claim 83, further comprising:
(c) planting the seed and growing a modified Triticum plant therefrom, wherein the modified Triticum plant comprises the recombinant nucleic acid molecule and has increased resistance to at least one PST race as compared to the unmodified Triticum plant, plant part, or cell.
85. (New) A modified Triticum plant, plant part, or cell produced by the method of claim 73, optionally wherein the modified Triticum plant part is a seed.
86. (New) A progeny plant, plant part, or cell produced by the method of claim 75, optionally wherein the progeny plant part is a seed.
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 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.
/REBECCA STEPHENS/Examiner, Art Unit 1663
/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
1 Pages 6 and 67 of the specification.
2 Page 6 of the specification.
3 Pages 6 and 67 of the specification.
4 Specification at the paragraph bridging pages 1-2 stating “[w]hile Yr5 confers resistance to almost all tested PST isolates worldwide, both Yr7 and YrSP have been overcome in the field following wide deployment (Table 1) and each display a different recognition specificity”.
5 See specification at page 15, lines 26-28.
6 See specification at page 22, lines 20-24.
7 See Page 22, lines 20-24 of the specification.
8 See specification at page 15, line 26 to page 16, line 7. Note that the BED_I structure (which is described as being present within all of YrSP, Yr5, and Yr7) is said to “confer PST resistance and is required for Yr7-mediated resistance” (specification at page 18, line 15).
9 See Page 22, lines 20-24 of the specification.
10 See Feng et al. 2015 Phytopathology 105(9): 1206-1213, of record IDS 25November2020; Zhang et al. 2009 Thero Appl. Genet 120:25-29.
11 ZHENG et al. “Evaluating the contribution of Yr genes to stripe rust resistance breeding through marker-assisted detection in wheat” 2017 Euphytica 213(50): 1-16 (16 total pages) DOI 10.1007/s10681-016-1828-6.
12 See Brini, Chapter 6: Genetic Transformation of Wheat: Current Status and Future Challenges in Agricultural Research Updates (Volume 13), 2016 Nova Science Publishers, Inc. (Gorawala and Mandhatri, Eds.) at page 106 and 121. See also He et al. 2015 J. Integrative Agriculture 14(3):438-452 at Abstract, paragraph bridging pages 438-439, second full paragraph on page 446, and the paragraph bridging pages 446-447.
13 KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at Pages 553-554.
14 KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at Pages 553-554.
15 Page 557, Right Column.
16 WO 2017/024053 published 09February2017.
17 MPEP § 2163(II)(A)(3)(a)(i).
18 MPEP § 2163(II)(A)(3)(a)(i) (citing Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406).
19 WO 2017/024053 published 09February2017.
20 MPEP § 2164.03.
21 MPEP § 2164.02(I).
22 MPEP § 2164.01(a) (citing In re Wands 858 F.2d 731 at 737; 8 USPQ2d 1400 at 1404 (Fed. Circ. 1988)).
23 Specification at the paragraph bridging pages 1-2 stating “[w]hile Yr5 confers resistance to almost all tested PST isolates worldwide, both Yr7 and YrSP have been overcome in the field following wide deployment (Table 1) and each display a different recognition specificity”.
24 See specification at page 15, lines 26-28.
25 See specification at page 22, lines 20-24.
26 See Page 22, lines 20-24 of the specification.
27 See, e.g., Feng et al. 2015 Phytopathology 105(9): 1206-1213, of record IDS 25November2020; Zhang et al. 2009 Thero Appl. Genet 120:25-29 at Abstract.
28 KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at Pages 553-554.
29 KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at Pages 553-554.
30 Page 557, Right Column.
31 WO 2017/024053 published 09February2017.
32 Specification at the paragraph bridging pages 1-2.
33 See Feng et al. 2015 Phytopathology 105(9): 1206-1213 at Abstract, of record IDS 25November2020; Zhang et al. 2009 Thero Appl. Genet 120:25-29.
34 See MPEP § 2164.06
35 WO 2017/024053 published 09February2017.
36 WO 2017/024053 published 09February2017.
37 WO 2017/024053 published 09February2017.
38 Specification at the paragraph bridging pages 1-2.
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