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 .
Election/Restrictions
The Office acknowledges the receipt of Applicant’s restriction election filed January 29, 2026. Applicant elects Group I, claim(s) 33-45, drawn to a method of producing a plant having an increase in a yield-related trait. Accordingly, Applicant elects: The method step of claim 33(a) as the “one method step from claim 33 (a) or (b), SEQ ID NO: 6 as the “one SEQ ID NO. from claim 36. Because no traverse is presented, this election is treated as election without traverse. The restriction is made FINAL
Claim Status
Claims 33-52 are pending.
Claims 46-52 are withdrawn as a result of Restriction Requirement.
Claims 33-45 are examined on the merits.
Claim Objections
Claim 44 is objected to as containing a grammar and punctuations error in the phase “selected from one or more of…..”.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 33-45 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.
Claims 33, 34, and 36-38 are rejected as indefinite for the claims 33, 34, 37 and 38 recitation “….RKD transcription factor or a variant or active fragment thereof..”; claim 36 recitation “RKD comprises.. any SEQ ID NO…..or a functional variant thereof”; about the term “RKD”, “active fragment”, “functional variant”.
The specification states that “‘RKD’ transcription factors, a subfamily of plant-specific RWP-RK transcription factors, control the formation of axillary meristems which determine several important traits of crop species” (paragraph 0008). However, this statement does not provide objective boundaries for determining what qualifies as an “RKD transcription factor”. In particular, although the specification identifies RKD transcription factors as a subfamily of plant-specific RQP-RK transcription factors, neither the claims nor the cited definition set forth the criteria of membership in that subfamily. For example, the claims do not identify what structural characteristics, sequence identity threshold, conserved domains beyond the broader RWP-RK transcription factors, neither the claims nor the cited definition set forth the criteria for membership in that subfamily.
Accordingly, it is unclear whether the term “RKD transcription factor” is limited to specifically disclosed proteins, to proteins expressly named RKD, to all members of a putative RKD subfamily in any plant species, or to any plant-specific RWP-RK transcription factor that may affect yield-related traits or axillary meristem formation. It is further unclear whether a gene or protein not expressly named RKD, but belonging to the broader RWP-RK transcription factor family or alleged to perform a similar function, falls within the scope of the claims. Thus, one of ordinary skill in the art would not be reasonably apprised of the metes and bounds of the claimed RKD transcription factor.
The additional terms “active fragment”, and “functional variant” further render the claims in definite because the claims do not recite the required relationship between such subject matter and the underlying RKD transcription factor with reasonable certainty. The terms “active fragment” and “functional variant” are indefinite because they rely on undefined functional language that fails to provide clear claim boundaries. Although “variant” and “fragment” may denote altered or truncated forms of a parent molecule, the additional modifiers “active” and “functional” do not specify what activity or function is required, how that activity is measured, or what degree of activity is sufficient. For example, it is unclear whether the required activity is membership in the RKD subfamily, DNA-binding activity, transcriptional regulatory activity, control of axillary meristem formation, increase in RKD transcription factor expression, or increase in a yield-related trait. Because no objective standard is provided for determining whether a given altered protein remains an RKD transcription factor variant, active fragment, or functional variant, as a result, a person of ordinary skill in the art would not be able to determine with reasonable certainty whether a given molecular is encompassed by the claims.
Dependent claim 35 is included in this rejection because the added RWPHRK motif does not cure the lack of clarity in the term “RKD transcription factor”, which remains without objective boundaries.
Dependent claims 39, 41 and 43 are included in this rejection because the recited transcription factors “RKD1, RKD2, RKD3, RKD4, and RKD 10”, “RKD6a, RKD6b, RKD9, and RKD11”, and “TaRKD1, or TaRKD4” are identified only by name, without sufficient objective boundaries such as sequence, accession, SEQ ID NO, or other identifying characteristics.
Dependent claims 40 and 42 are likewise indefinite because, although it narrows claim by reciting specific designations such as “TaRKD1-7a, TaRKD1-7b, TaRKD1-7d; ….” and “TaRKD6a-2a, TaRKD6a-2b, TaRKD6a -2d; ….”, the specification does not provide reasonably certain boundaries as to whether these names denote the exact disclosed sequences only. The specification refers to specific sequences, including TaRKD1-7d (SEQ ID NO: 6), TaRKD1-7a (SEQ ID NO: 1), TaRKD1-7b (SEQ ID NO: 4), etc. These sequences are presented in parentheses following the broader class of RKD transcription factors. The use of parenthesis creates ambiguity as to how these sequences are intended to limit the claimed subject matter. First, the parenthetical listing can be interpreted as merely exemplary, indicting representative species within a broader genus of RKD transcription factors, rather than limiting the scope of those specific sequences. Second, the parenthetical listing can be interpreted as optional, such that the claim encompasses RKD transcription factors generally, with or without the specifically recited sequences. Third, the parenthetical listing can be interpreted as suggesting equivalence, implying that the recited sequences are interchangeable with other members of the broader class that share similar structure or function. To the extend the specification presents such sequences in a non-limiting manner, it remains unclear whether the claim is restricted to the specific recited SEQ ID NOs or also encompasses sequence variants, related homologues, or other molecules associated with the same designations. Accordingly, one of ordinary skill in the art would not be able to determine the sequences with reasonable certainty.
Dependent claims 44-45 are included in this rejection because they do not add additional limitation to resolve the ambiguity.
Claims 34, 35, 39, 41, 43, and 45 are rejected as indefinite for the recitation “preferably”. The term “preferably” is a subjective, precatory descriptor and it is ambiguous whether the recited “preferably” features are required limitations or merely optional examples. Because the metes and bounds of the claim cannot be determined with reasonable certainty, i.e., whether the claim requires or merely suggests, the claim is indefinite.
Depend claims 40 and 42 are included in this rejection because they do not add additional limitation to resolve the ambiguity.
Claim 44 is rejected as indefinite for the recitation “the yield-related trait is selected from one or more of: (i) number of axillary meristems; (ii) number of tillers; (iii) rachis length; (iv) spike length; (v) number of spikelets per spike; (vi) number of grains per spike;(vii) panicle branch number; (viii) seed weight and/or number of seeds; and/or (ix) thousand kernel weight”.
Claim 44 appears to invoke a Markush Grouping by reciting a trait “selected from”. A Markush grouping is a closed group of alternatives, i.e., the selection is made from a group “consisting of” (rather than “comprising” or “including”) the alternative members. Abbott Labs., 334 F.3d at 1280, 67 USPQ2d at 1196. If a Markush grouping requires a material selected from an open list of alternatives (e.g., selected from the group “comprising” or “consisting essentially of” the recited alternatives), the claim should generally be rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim. See In re Kiely, 2022 USPQ2d 532 at 2* (Fed. Cir. 2022). In the instant case, the claim does not explicitly recite a group “consisting of”, therefore failing to render the grouping as a closed group of alternatives.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Descriptions
Claims 33-45 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has clarified the application of the written description requirement. The court stated that a written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not description of that material". Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
The claims are rejected for lacking adequate written description support regarding the broad scope of the following.
Claims 33 and the dependent claims 34-45 regards “a modified plant, part, cell or protoplast thereof having an increase in a yield-related trait.. RDK… a variant or active fragment” for “having an increase in a yield-related trait”.
Broad genus:
Claim 33 broadly encompasses a modified plant, plant part, cell, or protoplast “having an increase in a yield-related trait”, by obtaining a modified plant/material having increased RKD (including “variant”, “active fragment”, or “functional variant”) expression, and optionally regenerating. Dependent claims further expand the scope to RKD TFs defined by a short motif RWPHRK (claim 35); RKD TFS comprising any one of SEQID NO: 1, 4, 6-39 or a “functional variant” (claim 36); claims 37 and 38 broaden the scope further by reciting “reproductive RKD transcription factors”, again without clear structural boundaries. Claims 39-43 attempt to narrow the invention by naming particular RKD members or designations (e.g., RKD1-RKD11, TaRKD, AetRKD variants), but these designation are largely identified by name rather than by clearly defined structural characteristics, as discussed in the 112(b) rejection. Claims 44 and 45 expand the scope of the invention by reciting multiple yield related traits (e.g., tiller number, spikelet number, grain number, seed weight etc.) and extending the method to multiple crop plants including wheat, rice, barley, oat, maize, sorghum, and any plant parts/cells/protoplasts.
Contrast with what the specification actually shows:
The specification’s “yield” support is presented in a limited set of concrete working examples: (1) TaRKD1 overexpression in haploid wheat with increases in effective tillers, axil number, spikelet number, grains per spike, total seed weight per plant, and 1000-grain weight (Example 3, paragraph 0333-0340); (2) OsRKD3 overexpression in rice with increase in tiller number, panicle branch number, seeds per panicle, seeds per plant, and grain yield (Example 6, paragraph 0352-0353); (3) AtRKD4 overexpression in Arabidopsis reported to increase tiller number and axil number (Example 8, 0357-0358).
By contrast, the claims cover any RKD TF (including variants, active fragments, functional variants); many plant species and tissue types; and a long list of yield-related traits, without commensurate disclosure of which RKDs, which structures, and which modification reliably produce each claimed yield-related increase across the full scope.
Structure-function gap:
For the full claimed genus, the specification does not identify the essential structural features/common characteristics that make an RKD TF (or variant/fragment) capable of increasing a yield-related trait across the claim scope.
With respect to structure-function correlation, the specification does not identify the essential structural features or common characteristics that make an RKD transcription factor, or a claimed variant/fragment thereof, capable of producing the required functional result, namely an increase in a yield-related trait across the full scope of the claims. The specification defines RKD transcription factors as “a subfamily of a plant specific RWP-RK transcription factors’ and claim 35 further relies on the short motif RQPHRK. However, neither the specification nor the claims explain what structural characteristics, beyond belonging to that broad family or containing that short motif, distinguish those RKD proteins that allegedly increase yield-related traits from other related RWP-RK proteins, or from RKD-like variants and fragments, that would not. The art recognizes that the broader RWP-RK family contains distinct subfamilies, including RKD and NLP, and that the shared RWP-RK motif is a family-level DNA-binding feature rather than a disclosed predictor of the claimed yield-increasing phenotype. Chardin (Camille Chardin et. al., Journal of Experimental Botany (2014) Vol. 65, No. 19, pp. 5577–5587) describe the plant-specific RWP-RK family as comprising multiple groups with diverse biological roles, including nitrogen response and gametophyte development not a unified structure-function role for increased yield (page 5577, Abstract).
The specification itself illustrates this structure-function gap. In example 7 (paragraph 0354-0356) and Table 1 (paragraph 0355), the application identifies numerous rice genes encoding proteins with RWP-RK domains, including OsRKD1, OsRKD3, OsRKD4, OsRKD5, OsRKD6, OsRKD7, OsRKD8, OsRKD9, OsRKD10, as well as NLP family transcription factors. Yet among those many related proteins, the specification experimentally characterizes only OsRKD3 as producing the claimed yield-related phenotype. Thus, the disclosure itself shows that proteins sharing the relevant family/domain features are numerous, but it does not disclose what common structural characteristics distinguish the subset that will increase yield-related traits from those that will not (paragraph 0354-0355).
Nor does the specification demonstrate that closely related RKD family members predictably share the same function. The working examples provide data for only a few specific full-length proteins-TaRKD1 in wheat, OsRKD3 in rice, and AtRKD4 in Arabidopsis, under overexpression conditions (paragraph 0333-0340, 0352-0353, and 0357-0358). But the art indicates that RKD family members can have distinct developmental roles and expression patterns rather than a single conserved structure-function relationship. Tedeschi (Francesca Tedeschi et. al., New Phytologist (2017) 213: 1909–1924) reports that Arabidopsis RKD genes are expressed at distinct stages of embryo sac development and are involved in control of cell differentiation and normal gametophytic development (page 1909, Summary). Koi (Satoshi Koi et. al., Current Biology (2016) 26, pp1775–1781) likewise describe an evolutionarily conserved RKD factor as controlling germ cell differentiation (page 1775, Summary). These teaching support that RKD family membership does not , by itself, define a structurally predictable class of proteins that increase yield-related traits.
The claims are broader still because clams 33, 34, and 36-38 encompass variants, functional variants, and active fragments. However, the specification does not provide objective structural boundaries for such embodiments. It does not disclose what degree of substitution, deletion, insertion, truncation, or fragment length preserves the alleged yield-increasing function, nor does it identify any rule correlating such altered structures with the required phenotype. The examples ae limited to specific overexpression constructs of specific identified genes; the specification does not provide representative data showing that fragments, sequence variants retain the claimed function of increasing a yield-related trait (paragraph 0332-0241, -351-0353, and 0356-0358).
Thus, the disclosure does not reasonably convey possession of the claimed genus of “RKD transcription factor/variant/variant/active fragment” that achieves an increase in a yield-related trait.
Representative species/genus size (Eli Lilly-type analysis):
The claims recite a large functional genus defined primarily by result (increase in a yield-related trait) and broad identifiers (motif RWPHRK; a list of many SEQ ID NOs; reproductive /vegetative subclasses; multiple crops). The specification provides only a limited number of representative working species/constructs showing “yield-related” effects (TaRKD1-OX in wheat, OsRKD3-OX in rice, and AtRKD4-OX in Arabidopsis).
That limited disclosure is not reasonably representative of the full set of SEQ ID NO:1, 4, 6-39 and their claimed “functional variants”; active fragments and variants generally; and full range of yield-related traits and crop species recited.
Accordingly, the specification does not demonstrate possession of the full scope of claims 33-45 as of the filling date.
Scope of Enablement
Claims 33-45 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for certain narrow embodiments within the claims, namely the specifically exemplified overexpression of particular full-length RKD transcription factors in the disclosed plant systems (e.g., TaRKD1 in wheat, OsRKD3 in rice, and AtRKD4 in Arabidopsis), does not reasonably provide enablement for the full scope of the claimed invention, namely, the broader genus of methods using any RKD transcription factor (or variant or active fragment thereof) across multiple plants/plant parts/cells/protoplast to achieve an increase in any recited yield-related trait. 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 and use the invention commensurate in scope with these claims.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(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;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
Claims 33 and depend claims 34-45 regards the “a modified plant, part, cell or protoplast thereof having an increase in a yield-related trait.. RDK… a variant or active fragment” for “having an increase in a yield-related trait”.
The claims require enabling the POSITA to practice the invention across the entire scope, including multiple plant types (wheat, rice, barley, oat, maize, sorghum; and “plant part, cell, protoplast”); multiple yield-related traits (claim 44); multiple RKD TFs (including all listed SES ID NOs); other RKDs; RDK variants/fragments.
The specification is enabling only for certain narrow, specifically exemplified embodiments within the claim scope, namely ectopic overexpression of specific full-length RKD transcription factors in specific disclosed plant systems, such as TaRKD1 in hexploid wheat (paragraph 0332-0341), OsRKD3in rice (paragraph 0351-0353), and AtRKD4 in Arabidopsis (paragraph 0356-0358). In those specific embodiments, the application reports increases in certain yield-related traits such as tiller number, axil number, spikelet number, grains per spike, panicle branch number, seed number, seed weight, and/or thousand kernel weight. However, the claims are not limited to those specific tested embodiments. Instead, the claims encompass methods using any RKD transcription factor, including variants, functional variants, and active fragments thereof, across broad plant, plant part, cell, and protoplast contexts.
To achieve the claimed results of “an increase in a yield-related trait” across that full scope, a person of ordinary skill in the art would need to engage in substantial screening and optimization not taught by the specification. First, such a person would need to determine which RKD transcription factor among the broad number encompassed by the claims will produce the claimed phenotype in a given plant background. The specification itself shows the breadth problem. For example, Example 7/Table 1 identifies numerous rice genes encoding proteins with RWP-RK domains, including OsRKD1, OsRKD3, OsRKD4, OsRKD5, OsRKD6, OsRKD7, OsRKD8, OsRKD9, OsRKD10, as well as NLP family transcription factors (paragraph 0354-0355). Yet the specification experimentally demonstrates the claimed yield-related phenotype for only OsRKD3, not for the remaining listed RKD proteins and not for the NLP proteins. Thus, the disclosure itself evidences that a person of ordinary skill in the art would need to screen among numerous relate candidate proteins to determine which ones actually produce the claimed increase in yield-related traits.
Second, the claims extend beyond specific full-length tested proteins to include variants, functional variants, and active fragments, but the specification does not provide sufficient guidance to determine which such altered molecules retain the required function. The disclosure does not identify what amino acid substitutions, insertions, deletions, truncations, or fragment boundaries preserve the ability to increase a yield-related trait. Nor does the specification disclose any tested fragment or variant that was shown to produce the claimed phenotype. Rather, the working examples are directed to specific identified overexpression constructs of specific genes, such as TaRKD1, OsRKD3, and AtRKD4 (paragraph 0332-0341, 0351-0353, 0356-0358). Thus, a person of ordinary skill in the art would have to perform substantial experimentation to design and test which claimed variants, functional variants, or active fragments remain operative.
Third, the claims require not merely expression of an RKD-related molecule, but obtaining “a modified plant, part, cell or protoplast thereof having an increase in a yield-related trait relative to a reference”. That result is broad and claim 44 identifies multiple distinct trait endpoints, including number of axillary meristems; number of tillers; rachis length; spike length number of spikelets per spike; number of grains per spike; panicle branch number; seed weight and/or number of seeds; and/or thousand kernel weight. The specification reports certain measured increases for certain specific overexpression lines in certain species, but it does not provide a general teaching by which a person of ordinary skill in the art could predictably achieve any such increase across the full scope of claimed RKD factors, variants, fragments, plant materials, crops, and trait endpoints. Thus, substantial experimentation would be required to determine whether a particular claimed embodiment actually achieves the required measurable increase relative to a reference.
Forth, the nature of the invention and the state of the disclosure further support that such experimentation would be undue rather than routine. This is a biological genus claim in which success depends on the functional behavior of different transcription factors, altered protein forms, plant backgrounds, and phenotypic endpoints. The specification provide only a limited number of working examples and does not provide a predictive rule that would allow a skilled artisan to extrapolate from the disclosed embodiments to the full breadth of the rejected claims. In particular, the disclosure does not teach how to predict, from RKD family membership alone, which untested RKD transcript factors, variants, or fragments will produce the claimed increase in yield-related traits.
Accordingly, the specification does not enable a POSITA to make any use the full scope of claims 33-45 without undue experimentation, particularly with respect to achieving an increase in a yield-related trait across the claimed RKD/variant/fragment, plant materials, crops, and trait endpoints.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 33-39 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Waki (Takamitsu Waki et. al., Current Biology (2011)21, 1277–1281).
Claim 33 recites a method of producing a modified plant, part, cell or protoplast thereof having an increase in a yield-related trait relative to a reference plant, part, cell or protoplast thereof, comprising:(a) Providing the plant, part, cell or protoplast thereof with an RKD transcription factor or a variant or active fragment thereof, or a polynucleotide encoding said RKD transcription factor, variant or active fragment thereof; and (c) Obtaining a modified plant, part, cell or protoplast thereof having an increase in RKD transcription factor expression. Since step (b) is an alternative to step (a), it is not included in this rejection.
Under a broadest reasonable interpretation for purposes of this rejection, “having an increase in a yield-related trait relative to a reference plant, part, cell or protoplast thereof..” encompasses an increase in a trait that contributes to yield by increasing organ-forming capacity, including increased meristematic or embryogenic growth capacity (e. g., increased formation/maintenance of proliferative meristematic/embryogenic tissues), relative to an otherwise comparable reference.
Step (a) encompasses introducing an RKD transcription factor or a nucleic acid encoding the RKD protein into plant material such that RKD is expressed. Step (c) requires obtaining plant material exhibiting increased RKD expression (e.g., ectopic/overexpression) relative to a reference.
Waki discloses that RKD4 (a plant RWP-RK/RKD transcription factor) is preferentially expressed in early embryos and that overexpression of RKD4 in seedlings ectopically induces early embryo-specific genes and primes somatic cells for embryogenesis (page 1277 Summary), evidencing that providing an RKD transcription factor (or a polynucleotide encoding same) results in increased RKD expression in plant tissues.
Waki further discloses that “indRKD4ox seedlings enhanced cell proliferation in the regions normally rich in cycling cells, such as the root meristem and young leaf primordia”( page 1279 paragraph 2), demonstrating increased proliferative activity in meristematic/organ-initiating regions upon increased RKD expression.
Therefore, Wake discloses a modified plant/plant tissue exhibiting an increase in a yield-related trait relative to a reference, in addition to disclosing an RKD transcription factor (or polynucleotide encoding same) and obtaining increased RKD expression.
Accordingly, Waki discloses each and every element of claim 33, and therefore anticipates claim 33 under 35 USC § 102(a)(1).
Claim 34 depends from claim 33 and specifies that step (a) comprises introducing “the RKD transcription factor protein…or a polynucleotide encoding said RKD transcription factor…into the plant, plant part, cell or protoplast”, preferably by transforming/transducing.
Waki discloses introducing a polynucleotide encoding an RKD transcription factor into plant material because Waki “generated a transgenic line, designated indRKD4ox, which allows overexpression of RKD4 upon induction by dexamethasone (DEX)” (page 1278 last paragraph). The creation and use of an overexpression transgenic line necessarily requires that a polynucleotide encoding RKD4 was introduced into the plant/plant cells, thereby meeting claim 34’s “introducing…a polynucleotide encoding said RKD transcription factor…into the plant /plant part/cell” limitation.
Accordingly, Waki discloses each and every element of claim 34, and therefore anticipates claim 34.
Claim 35 depends from claim 33 and requires that the RKD transcription factor comprises an amino acid sequence comprising the motif RWPHRK (SEQ ID NO:2).
Waki disclose Arabidopsis RKD4 (AT5G53040) and describes RKD4 as an RQP-RK motif-containing protein/transcription factor (page 1277, Result, first paragraph) (see sequence information below).
Further, the protein sequence of RKD4 (AT5G53040) includes the motif RQPHRK, which corresponds to SEQ ID NO:2.
Therefore, Waki’s RKD4 meets the RKD transcription factor motif limitation of claim 35.
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Claim 36 depends from claim 33 and recites that “the RKD transcription factor comprises an amino acid sequence according to any one of SEQ ID NO: 1, 4, 6-39 or a functional variant thereof”.
Waki discloses the RKD transcription factor RKD4 (AT5G53040) (page 1277, Result, first paragraph). The RKD4 protein sequence of AT5G53040 corresponds to the amino acid sequence of AtRKD4 (SEQ ID NO: 39) as disclosed in the instant application (see alignment below).
Because Waki discloses an RKD transcription factor having the amino acid sequence of SEQ ID NO:39, Waki meets the limitation of claim 36.
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Claim 37 depends from claim 33 and requires that “the RKD transcription factor is a reproductive RKD transcription factor”, and optionally states that step (a) comprises providing a vegetative tissue (or vegetative cell/protoplast) with the reproductive RKD transcription factor (or polynucleotide encoding same).
Waki discloses Arabidopsis RKD4 (AT5G53040), an RWP-RK/RKD transcription factor, that is transcribed preferentially in early embryos and functions in embryogenesis, “RKD4 was transcribed preferentially in early embryos” and rkd4 mutants show embryo defects (Summary and Result section).
Under BRI, an RKD transcription factor that is preferentially expressed in early embryos and regulates early embryogenesis is a reproductive RKD transcription factor. Thus, Waki RKD4 meets the “reproductive RKD transcription factor” limitation of claim 37.
Further, Waki also discloses the optional embodiment, because Waki generated an inducible overexpression line (indRKD4ox) and overexpressed RKD4 in seedlings (vegetative tissue), where RKD4 overexpression enhanced cell proliferation in root meristem and young leaf primordia and primed somatic cells for embryogenesis (page 1279, paragraph 1-3).
Claim 38 depends from claim 37 and recites that step (a) comprises ectopically expressing the reproductive RKD transcription factor (or a variant/active fragment thereof, or a polynucleotide encoding same) in vegetative tissue of a plant, plat part, cell or protoplast.
For the reasons set forth above with respect to claims 33, 34, and 37, Waki further discloses ectopic expression of RKD4 in vegetative tissue, because Waki generated a transgenic line “indRKD4” that allows overexpression of RKD4 in seedlings (vegetative tissue) upon induction by dexamethasone (DEX)( page 1279, paragraph 1-3).
Claim 39 depends from claim 37 and recites the method according to claim 37, wherein the reproductive RKD transcription factor is selected from RKD1, RKD2, RKD3, RKD4, and RKD 10, preferably wherein the reproductive RKD transcription factor is selected from TaRKD1, TaRKD3,TaRKD4, TaRKD10, AetRKD1, AetRKD3, and AetRKD4.
Waki discloses the RKD transcription factor RKD4 (AT5G53040) (page 1277, Result, first paragraph), which corresponds to the amino acid sequence of AtRKD4 (SEQ ID NO: 39). AtRKD4 belongs to RKD4 transcription factor.
Accordingly claims 34-38 are anticipated by Waki.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 33-40, and 43-45 are rejected under 35 U.S.C. §103 as being unpatentable over Waki (2011), in view of Koszegi (Dávid Koszegi et. al., The Plant Journal (2011) 67, pp280–291) and Bommert (Peter Bommert et. al., NATURE (2013) VOL 502, pp555-558).
For purposes of the 103 rejection of claim 33-38, and 43-45, the phrase “having an increase in a yield-related trait relative to a reference plant, part, cell or protoplast thereof..” is interpreted under BRI consistent with the claims as a whole, including dependent claim 44, as follows: “yield-related trait” encompasses agronomic yield components and plant architecture traits that contribute to yield, including at least one of the traits expressly recited in claim 44, such as: (i) number of axillary meristems; (ii) number of tillers; (iii) rachis length; (iv) spike length; (v) number of spikelets per spike; (vi) number of grains per spike;(vii) panicle branch number; (viii) seed weight and/or number of seeds; and/or (ix) thousand kernel weight.
Claim 33 recites a method of producing a modified plant, part, cell or protoplast thereof having an increase in a yield-related trait relative to a reference plant, part, cell or protoplast thereof, comprising:(a) Providing the plant, part, cell or protoplast thereof with an RKD transcription factor or a variant or active fragment thereof, or a polynucleotide encoding said RKD transcription factor, variant or active fragment thereof; and (c) Obtaining a modified plant, part, cell or protoplast thereof having an increase in RKD transcription factor expression.
Waki teaches that RKD4 (a plant RWP-RK/RKD transcription factor) is a transcription factor preferentially expressed in early embryos, and that overexpression of RKD4 in seedlings ectopically induces early embryo-specific genes and “primes somatic cells for embryogenesis” (page 1277 Summary). Waki further teaches “indRKD4ox seedlings enhanced cell proliferation in the regions normally rich in cycling cells, such as the root meristem and young leaf primordia” (page 1279 paragraph 2), evidencing a developmental reprogramming outcome upon increased RKD expression. Furthermore, a POSITA would understand that meristematic regions are defined by actively cycling, undifferentiated cells, and that leaf primordia are initiated from the flanks (peripheral zone) of the shoot apical meristem. Therefore, Waki evidences modulation of meristematic cell cycling and SAM-driven organ initiation, which is directly relevant to shoot meristem activity and downstream shoot branching/tiller development.
Waki does not teach that overexpression an RKD gene increases agronomic yield traits such as seed yield, grain number, grain weight, biomass production, harvest index, or tiller/branch number relative to a reference plant.
Koszegi teaches that AtRKD1 and AtRKD2 are preferentially expressed in egg cells, and that ectopic expression of AtRKD1/ AtRKD2 induces cell proliferation and expression of an egg-cell marker, and that RKD-induced proliferating cells show a shift toward an egg-cell-like transcriptome (page 280 Summary, page 286 Discussion). Koszegi further teaches that ectopic expression of RKD factors generates proliferating, undifferentiated tissues and activates an egg cell-related transcriptional program, indicating that RKD transcription factors are capable of reprogramming plant cells and promoting proliferative developmental stages (page 286 Discussion; fig 4-6). Such proliferative cellular states are characteristic of meristematic tissues in plants, which consist of actively dividing undifferentiated cells that give rise to plant organs. Thus, Koszegi teaches that manipulation or ectopic expression of RKD transcription factors can alter developmental programs and promote proliferative cell states associated with meristematic activity.
Bommert teaches “the inflorescence meristem was enlarged, leading to extra rows of SPMs (spikelet pair meristems), and SPMs branch to generate a pair of spikelet meristems in adjacent vertical rows, corresponding to rows of seeds in the cob” (page 555, right collum paragraph 2). The Kernel rows are initiated by the inflorescence shoot meristem, increasing inflorescence meristem size increases kernel row number (a yield component) (page 557, right column paragraph 2). Bommert therefore demonstrates that modulation of meristem developmental activity directly alters inflorescence architecture and kernel row number, and recognized yield-related trait in maize.
Accordingly, because Koszegi teaches that RKD transcription factors can induce proliferative developmental programs in plant cells, and Bommert teaches that modulation of meristem activity determines kernel row number and plant productivity, a person of ordinary skill in the art would have understood that altering developmental regulators capable of inducing proliferative cell states would be expected to influence meristem developmental programs. Because meristem size and activity determine kernel row number and other yield-related traits, it would have been obvious to employ transcriptional regulators such as RKD factors to modify plan developmental programs in order to obtain plants exhibiting altered yield-related traits, including increased kernel row number.
With respect to step (a) of claim 33, Waki teaches providing a polynucleotide encoding an RKD transcription factor by induced overexpression of RKD4.
With respect to step (c) of claim 33, Waki teaches induced overexpression of RKD4 (increased RKD expression relative to a reference), and Koszegi teaches ectopic RKD expression produces proliferating cells and egg-cell marker expression (an observable phenotype consistent with increased RKD activity/expression).
A person of ordinary skill in the art would have been motivated to apply the RKD overexpression approach of Waki/ Koszegi to obtain plants with yield related trait changes because Waki and Koszegi teach RKD factors are developmental regulators whose increased expression can reprogram cell fate, enhanced cell proliferation in the regions normally rich in cycling cells (such as meristem regions), and induce ectopic proliferating cell population, while Bommert teaches that yield components (e.g., kernel row number) depend on inflorescence meristem size/activity and that increasing meristem size increases kernel row number with yield potential. Accordingly, a POSITA would have reasonably expected that increasing expression of a development regulator such as RKD-shown to induce proliferating development programs, would affect meristem-derived yield components.
Claim 36 is drawn to the method according to claim 33, wherein the RKD transcription factor comprises an amino acid sequence according to any one of SEQ ID NO: 6 or a functional variant thereof.
For the same reasons set forth with respect to claim 33, and following species election, claim 36 is directed to an RKD transcription factor comprising SEQ ID No:6 or a functional variant thereof.
Koszegi teaches a TaRKD2 (JF714947) (page282, fig 1) gene, which is 100% identical with SEQ ID NO: 6 (alignment below). TaRKD1-7d (SEQ ID NO: 6) (paragraph 0081).
Waki, Koszegi and Bommert teach each and every limitation of claim 36, including the RKD transcription factor comprising SEQ ID NO:6. Claim 36 is obvious over Waki, Koszegi and Bommert.
Claim 34 depends from claim 33 and specifies that step (a) comprises introducing “the RKD transcription factor protein…or a polynucleotide encoding said RKD transcription factor…into the plant, plant part, cell or protoplast”, preferably by transforming/transducing.
Waki teaches introducing a polynucleotide encoding an RKD transcription factor into plant material because Waki “generated a transgenic line, designated indRKD4ox, which allows overexpression of RKD4 upon induction by dexamethasone (DEX)” (page 1278 last paragraph). The creation and use of an overexpression transgenic line necessarily requires that a polynucleotide encoding RKD4 was introduced into the plant/plant cells, thereby meeting claim 34’s “introducing…a polynucleotide encoding said RKD transcription factor…into the plant /plant part/cell” limitation.
Claim 35 depends from claim 33 and requires that the RKD transcription factor comprises an amino acid sequence comprising the motif RWPHRK (SEQ ID NO:2).
Koszegi teaches a TaRKD2 (JF714947)(page282, fig 1) gene, and contains “RWPHRK” motif (sequence below).
Claim 37 depends from claim 33 and requires that “the RKD transcription factor is a reproductive RKD transcription factor”, and optionally states that step (a) comprises providing a vegetative tissue (or vegetative cell/protoplast) with the reproductive RKD transcription factor (or polynucleotide encoding same). Claim 38 depends from claim 37 and recites that step (a) comprises ectopically expressing the reproductive RKD transcription factor (or a variant/active fragment thereof, or a polynucleotide encoding same) in vegetative tissue of a plant, plat part, cell or protoplast.
Koszegi teaches egg-cell-associated RKD factors and that ectopic expression induces proliferating cells and egg-cell marker expression, “TaRKD1 and TaRKD2 are preferentially expressed in the egg cell of wheat” (page 280, Summary). and Waki teaches overexpression in non-embryo context (seedlings) induces embryo-program expression (page 1279, left column, paragraph 1); thus, ectopic expression of reproductive-program RKD factors in vegetative tissues/cells is an obvious implementation of the RKD reprogramming approach.
Claim 39 depends from claim 37 and recites the method according to claim 37, wherein the reproductive RKD transcription factor is selected from RKD1, RKD2, RKD3, RKD4, and RKD 10.
Koszegi teaches a TaRKD2 (JF714947) (page282, fig 1) gene, “TaRKD1’ as used herein may be used interchangeably with ‘TaRKD2’. TaRKD2 is the old name for TaRKD1, therefore either of these names may be considered to be a reference to the same transcription factor” (paragraph 0058, current application). TaRKD2 (JF714947) belongs to RKD1 transcription factor. As set forth in the rejection of claim 36, TaRKD2 (JF714947) is TaRKD1-7d (SEQ ID NO: 6).
Claim 40 depends from claim 39, wherein the reproductive RKD transcription factor is selected from the group consisting of TaRKD1-7d.
As set forth in the rejection of claim 36 and 39, TaRKD2 (JF714947) is TaRKD1-7d (SEQ ID NO: 6).
Koszegi teaches a TaRKD2 (JF714947) (page282, fig 1) gene, which is 100% identical with SEQ ID NO: 6 (alignment below). TaRKD1-7d (SEQ ID NO: 6) (paragraph 0081).
With respect to claims 34, 35, and 37-40, it would have been obvious to one of ordinary skill in the art to implement the method of claim 33 by introducing an RKD transcription factor or a polynucleotide encoding it into plant material (claim 34), to use an RKD factor belonging to the plant-specific RWP-RK family (claim 35), and to employ a reproductive RKD transcription factor, including by ectopic expression in vegetative tissue (claims 37 and 38), with a reasonable expectation of obtaining altered proliferative/meristematic developmental programs and corresponding yield-related traits.
The claimed invention in claims 34, 35, 37, 38, and 39 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Claim 43 is drawn to the method of claim 33, wherein the RKD transcription factor is TaRKD1, or TaRKD4, preferably is selected from: TaRKD1-7d (SEQ ID NO: 6), TaRKD1 - 7a (SEQ ID NO: 1) and TaRKD1 - 7b (SEQ ID NO: 4), preferably is TaRKD1-7d (SEQ ID NO:6).
For the same reasons set forth with respect to claim 33, although the prior art designates the sequence as TaRKD2 (page282, fig 1) and the present application designates it as TaRKD1-7d (SEQ ID NO:6), sequence alignment shows 100% identity. Accordingly, the distinction is solely a difference in naming convention and does not represent a structural difference.
Waki, Koszegi and Bommert teach each and every limitation of claim 36, including the RKD transcription factor is TaRKD1-7d (SEQ ID NO:6). Claim 43 is obvious over Waki, Koszegi and Bommert.
Claim 44 is drawn to the method of claim 33, wherein the yield-related trait is selected from one or more of: (i) number of axillary meristems; (ii) number of tillers; (iii) rachis length; (iv) spike length; (v) number of spikelets per spike; (vi) number of grains per spike;(vii) panicle branch number; (viii) seed weight and/or number of seeds; and/or (ix) thousand kernel weight.
For the same reasons set forth with respect to claim 33, Bommert further teaches that variation in inflorescence meristem size affects kernel row number with the potential to increase yield (page 557, right column paragraph 2). Thus, Bommert teaches that alteration of meristem developmental programs predictably changes yield-related traits, including seed number-associated traits.
Claim 45 is drawn to the method of claim 33, wherein the plant is a crop plant, part, cell or protoplast thereof, preferably wherein the plant is selected from: wheat (Triticnae), rice (Oryza), barley (Hordeum), oat (Avena), maize (Zea) or sorghum (Sorghum), or parts, cells or protoplasts thereof.
For the same reasons set forth with respect to claim 33, Koszegi further teaches overexpress RKD in wheat (Triticnae) (page 280, Summary). Thus, Waki, Koszegi and Bommert teach application of RKD transcription factor biology and meristem/yield-related developmental regulation in crop species encompassed by claim 45, and would have been obvious to apply the method of claim 33 in crop plants.
The claimed invention in claims 44-45 as a whole is prima facie obvious over the combined teachings of the prior arts above.
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Conclusion
No claims are allowed.
Contact Information
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/YANXIN SHEN/ Examiner, Art Unit 1663
/WEIHUA FAN/ Primary Examiner, Art Unit 1663