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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 September 26, 2025 has been entered.
Status of the Claims
The amendments and arguments filed 26September2025 are acknowledged and have been fully considered.
For clarity of the record, Applicant re-wrote the claims 20December2024. Therein, and here with the claims dated 26September2025, claim 56 encompasses the subject matter of previously-pending claims 28-29, 33-36, and 38. As re-written 20December2024, and here with the claims dated 26September2025, claim 72 has consonance with non-elected Group VIII (see claim 27 of the claims dated 09October2020). Therefore, claim 72 REMAINS withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected group of invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 01July2022.
With the amendments 26September2025: claims 1-55 were previously canceled; claims 56-72 are pending; claim 72 is withdrawn; claims 57-71 were previously presented; and claim 56 is currently amended.
Claims 56-71 are examined on the merits herein.
Claim Interpretation & File History
[Copied from the Final Action Dated 28March2025 → ] 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 26September2025:
Applicant’s Remarks 26September2025 (hereinafter “Remarks”) at pages 6-7 and the second declaration by Dr. LAGUDAH filed 26September2025 (hereinafter “LAGUDAH Declaration2”) at ¶¶21,25-30 both assert that these claims encompass introducing Yr5, Yr7, or YrSP by gene editing.
For the reasons set forth above, the concept of gene editing was already explicitly deleted from the claims (i.e., Applicant is trying to undo their own amendments to recapture the gene editing concept). The Office believes Applicant is estopped from doing so (for the reasons set forth above and of record, namely Applicant’s claim amendments which deleted “editing genomic material” from the claims), but even if gene editing is within these claims; the concept of gene editing does not remedy the Indefiniteness, Written Description, or Enablement issues discussed of record and maintained herein. For the sake of a clear record, please also note that (per Applicant’s arguments dated 27December2022) these claims do not encompass plant crosses/breeding (one will note that a prior art rejection over FENG et al. was withdrawn for that reason).
[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.
Withdrawn Objections and/or Rejections
Objections and/or rejections made of record in the final office action dated 28March2025 that are not otherwise discussed herein are withdrawn. In particular:
RE the paragraph at the top of page 4: The objection to claim 56 is withdrawn in view of the amendment to the claims.
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 26September2025:
Applicant asserts that the Office is mistaken (presumptively due to the Office not understanding the difference between a locus and a gene) (pages 8-9, see also ¶¶5-19 of the LAGUDAH Declaration2).
This is not persuasive. Please see the claim amendments proposed by the Examiner (attached to this action) for further clarification as to why these claims remain rejected here and how these indefiniteness issues may be remedied (e.g., deleting the “native locus” concept from the claims and specifying whether or not a plant comprises Yr5, Yr7, or YrSP on its nuclear 2BL chromosome).
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.
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:
Applicant asserts that the specification, as further explained by LAGUDAH Declaration2, sufficiently describes the full metes and bounds of these claims (e.g., the use of any regulatory element to transform, and express, Yr5, Yr7, and/or YrSP within a wheat plant) (pages 10-11, also citing ¶¶53-56 of the LAGUDAH Declaration2).
This remains unpersuasive. Applicant’s arguments and the LAGUDAH Declaration2 continue to emphasize the skill in the art such that a skilled artisan could figure it out (i.e., find a sufficient combination of Yr5, Yr7, and YrSP and a sufficient promoter that, when introduced and expressed within a later-identified parental genomic background, will increase/enhance the transformed plant’s PST resistance to at least one PST race as compared to the untransformed parental plant) which is not sufficient for Written Description.
The LAGUDAH Declaration2 takes particular issue with the Office supposedly not “provid[ing] any objective evidence that the nucleic acids encoding Yr5, Yr7, or YrSP polypeptides can’t be expressed from any promoter, but merely makes unsubstantiated, conclusory assertions” (¶55 on page 13).
The Office’s position regarding regulatory elements (in particular, promoters) remains focused on the lack of information within the as-filed specification. The Office, as always for Written Description and Enablement analysis, has also searched the prior art to find some evidence supporting the breadth of these claims. The Office still cannot find prior art experiments describing recombinant constructs for Yr5, Yr7, or YrSP gene expression within a wheat plant/part (= the deficiencies of the specification remain uncompensated by the prior art) and the Office has looked for tangential evidence regarding Yr5, Yr7, or YrSP expression which a skilled artisan would utilize in choosing regulatory elements such as promoters (tangential evidence such as gene expression profiles, such as transcriptome analysis), but has not identified clear evidence for all of Yr5, Yr7, and YrSP. For example, looking at the specification (line 24 on page 22) where it says that DNA was extracted “from leaf tissue at the seedling stage” and given what is generally accepted in the field now (i.e., post-filing) such as that Yr5, Yr7, and YrSP are “all-stage” PST resistance genes; it would seem like constitutive or leaf-specific expression may work for useful Yr5, Yr7, or YrSP expression to obtain increased/enhanced PST resistance? And, as indicated in the proposed claim amendments copied herein below and attached, it would of course be expected that the gene’s native/endogenous regulatory elements (e.g., promoter) may be used for recombinant expression (so long as those elements are sequenced) as had been done in the prior art for the Yr10 gene19. Even if the Office is correct (that a constitutive, leaf-specific promoter, or native/endogenous promoter may be used to recombinantly express Yr5, Yr7, or YrSP), the Office is not in the best position to confirm that belief (Applicant is) and, in any event, these claims remain agnostic to regulatory elements and continue to encompass any type of promoter (etc.). Inducible promoters are encompassed, for example, but one must ask: induced by what? The Office does not see any information in the specification or prior art regarding what molecules innately induce Yr5, Yr7, or YrSP expression or the conditions under which these genes must be expressed in order to successfully confer PST resistance, so one cannot reasonably identify a useful inducible promoter for the claimed subject matter. It is notable that neither Applicant’s remarks nor the LAGUDAH Declaration2 attest to a particular type of promoter being useful for the claimed subject matter—both simply point out that the specification provides explicit reference to constitutive, strong, inducible, stress, and tissue-specific promoters and that a skilled artisan “is readily able to select suitable regulatory elements for gene expression”20—Applicant’s reluctance to commit to a particular type of promoter combined with Applicant’s reluctance to provide prior art evidence about what promoters would be reasonably expected to work for Yr5, Yr7, or YrSP expression together suggest that the Office is right: the breadth of regulatory elements (e.g., promoters) within these claims is not supported. Applicant should please consider adding regulatory element (e.g., promoter) particulars to the claims (see, e.g., the proposed claim amendments copied herein below and attached) and Applicant is reminded that Declaration practice may be useful for attesting to what a skilled artisan would reasonably know or expect at the time this application was filed (kind reminder to file an IDS if publications are being cited which are not already of record). Please also note that the breadth of regulatory elements (e.g., promoters) in these claims is not the only issue underlying this rejection = adding promoter particulars to the claims will not be enough to overcome this rejection.
The LAGUDAH Declaration2 restates that ZHENG et al. is not relevant to this issue because ZHENG et al. do not describe introducing Yr5 at a non-native locus within a wheat plant (¶¶50-52 at page 12).
The Office cites ZHENG et al. to evidence that, before this application was filed, it was known that different Yr genes confer different resistance profiles to a wheat plant (a Yr gene impacts the specific race(s) to which resistance is conferred as well as the strength of that resistance, as is shown in FIG 3 of ZHENG et al.). Further, different combinations of Yr genes confer disparate resistance profiles and resistance strengths (see FIG 4 of ZHENG et al.). The Office just used Yr5 as an example in the context of ZHENG et al. (i.e., the discussion of Yr5 in the context of ZHENG et al. can just as easily be amended to state Yr7 or YrSP). To that end, the following are alternative examples may be substituted into the rejection above and of record (using Yr5 is not critical for making the Office’s point):
“As shown by ZHENG et al., simply introducing Yr7 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 Yr7 thereinto).”
Or
““As shown by ZHENG et al., simply introducing YrSP 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 YrSP thereinto).”
Further to the discussion immediately above, the LAGUDAH Declaration2 also states that Yr6, Yr29, Yr30, Yr33, and/or Yr41 are distinct from Yr5, Yr7, and YrSP (¶¶51-52 at page 12).
The Office understands that point and agrees. Here again, the Office used Yr6, Yr29, Yr30, Yr33, and Yr41 as examples to elucidate the issues underlying this rejection. As a concrete example to ensure clarity, suppose the parent plant of these claims is a “AvS/PI 484480F7-128” wheat plant from FENG et al.21 which comprises Yr53 (discussed in ZHENG et al.) and further suppose that Yr7 is introduced thereinto (all of which is encompassed by these very broad claims). At least FENG et al. say that a AvS/PI 484480F7-128 plant is “resistant to all [ten tested] races but with slightly different [infection types]” whereas a plant comprising Yr7 (“AvSYr7NIL”) is “susceptible to all [ten tested] races, except resistant to PST-3”. With this example, and without more information from Applicant, a skilled artisan would not reasonably expect any increased/enhanced PST resistance from having introduced Yr7 into a “AvS/PI 484480F7-128” wheat plant (comprising the Yr53 resistance gene) because Yr53 confers a greater breadth and strength of PST resistance than does Yr7. And yet, again, this example is within the current claims.
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.
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”22); (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”23).24
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 specification25) 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.26 The plant breeding steps of the specification27 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.28 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.29 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)).30 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.31 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.32 These facts are exemplified in prior publications by the inventor(s): albeit with a different class of proteins, LAGUDAH et al.33 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 resistance34), 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)35 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 routine36—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:
Applicant’s arguments in response to this Enablement rejection are very similar to those presented for Written Description above (as is customary when the rejections are both based on the same facts or deficiencies). To that end, the Office will address Applicant’s comments which are different for this enablement rejection as compared to those for the Written Description rejection.
Applicant asserts that the claims are not limited to a particular parental plant (Remarks at page 13, LAGUDAH Declaration2 at ¶58 on page 14).
Setting aside the indefiniteness issue regarding the parental plants within these claims (and how to determine what “native locus” means), the Office agrees that these claims encompass a breadth of parental plants and the Office maintains that the breadth of parental plants within these claims is part of the problem underlying the Written Description and Enablement issues. Please review the proposed claim amendments (copied herein below and attached hereto) for an example of how clearly defining the “parental plants” concept in these claims can remedy all of the indefiniteness, Written Description, and Enablement issues on that point. In particular, again, please note that the structure/genomic background of the parent plant can contain anything (i.e., can contain any one or more Yr genes and, therefore, the parent plant can already have any PST-resistance profile). As a specific example to help illuminate the problem, the “parent plant” of these claims may be Fielder wheat and, because these claims remain broad with respect to what Yr gene is being introduced, these claims encompass introducing only Yr7 into a Fielder wheat parent plant (which the Office believes does not contain Yr7 innately and, therefore, meets the “native locus” concept of these current claims). Based on the current record, one such transformed plant (Fielder wheat + recombinant Yr7 gene) would not be expected to have an increased/enhanced PST resistance because Yr7 has “been overcome in the field following wide deployment”.37 Because the modified wheat plants of these claims (or obtained by the claimed methods) are said to have an increased/enhanced PST resistance as compared to the “parental” plant, these claims need to be tailored toward parental plants and Yr gene combinations that may reasonably confer increased/enhanced PST resistance. Applicant should note that the claims proposed by the Office (copied herein below and attached hereto) start with the introduction of just Yr5 because, according to the specification and art, Yr5 remains useful for PST resistance (a breadth of isolates/races) whereas Yr7 and YrSP do not. To that end, Applicant will further note that the “parental plant” concept is captured by saying that the plant into which Yr5 is introduced does not already comprise Yr5 and, in that way per the specification and prior art, a skilled artisan would reasonably expect the resulting modified plant to have increased/enhanced PST resistance (at least to certain isolates/races) via the new presence of Yr5 that it would have before Yr5 was introduced thereinto. For completeness, but unrelated to the “parental plant” concept, the promoter suggested by the Office is the endogenous/native Yr5 promoter (which, in view of the specification and prior art such as LIU et al.38, may be readily obtained by a skilled artisan and would be expected to work for recombinant expression of Yr5 in a wheat plant).
Applicant asserts, pointing toward the LAGUDAH Declaration2, that the amount of experimentation needed to practice the full breadth of the claimed subject matter would not have risen to the level of undue trial and error experimentation (Remarks at the middle of page 13 to page 15). The LAGUDAH Declaration2 specifically points toward the work of a graduate student (as evidenced by the ZHANG thesis) to supposedly show that practicing the full scope of these claims would not amount to undue trial and error experimentation (¶60 at pages 14-15 and ¶66 on page 16).
This is not persuasive at least because the breadth of work reported in the ZHANG thesis is not commensurate with the scope of these claims. Notably, ZHANG used Fielder wheat as the parental plant (which is believed to not comprise Yr5, Yr7, or YrSP genes) and ZHANG appears to have used native/endogenous promoters to transform (and express) Yr5 or YrSP (separately) therein (Yr7 was not tested and gene combinations were not tested). For completeness, the work by ZHANG also appears to have focused on a specific subset of PST isolates/races (i.e., ZHANG only conferred increased/enhanced PST resistance for particular isolates/races). As said of record and again here, these claims are much broader than the work summarized in the ZHANG thesis.
Conclusion
Please see the Interview Summary attached 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 this 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 attachments for those comments).
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.
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/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 LIU et al. “The Stripe Rust Resistance Gene Yr10 Encodes an Evolutionary-Conserved and Unique CC-NBS-LRR Sequence in Wheat” 2014 Molecular Plant 7:1740-1755. Cited because LIU et al. demonstrates recombinant expression of the Yr10 gene in wheat via transformation with an expression construct within which the Yr10 gene is expressed under the control of its native/endogenous Yr10 promoter.
20 LAGUDAH Declaration2 at ¶54 on page 13.
21 FENG et al. is of record (formerly the subject of an art rejection), see the top of the left column on page 1210 of FENG et al..
22 MPEP § 2164.03.
23 MPEP § 2164.02(I).
24 MPEP § 2164.01(a) (citing In re Wands 858 F.2d 731 at 737; 8 USPQ2d 1400 at 1404 (Fed. Circ. 1988)).
25 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”.
26 See specification at page 15, lines 26-28.
27 See specification at page 22, lines 20-24.
28 See Page 22, lines 20-24 of the specification.
29 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.
30 KUMLEHN and HENSEL “Genetic Transformation Technology in the Triticeae” 2009 Breeding Science 59:553-560 at Pages 553-554.
31 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.
32 Page 557, Right Column.
33 WO 2017/024053 published 09February2017.
34 Specification at the paragraph bridging pages 1-2.
35 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.
36 See MPEP § 2164.06
37 Specification at the paragraph bridging pages 1-2.
38 LIU et al. “The Stripe Rust Resistance Gene Yr10 Encodes an Evolutionary-Conserved and Unique CC-NBS-LRR Sequence in Wheat” 2014 Molecular Plant 7:1740-1755. Cited because LIU et al. demonstrates recombinant expression of the Yr10 gene in wheat via transformation with an expression construct within which the Yr10 gene is expressed under the control of its native/endogenous Yr10 promoter.