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/Restriction
The Office acknowledges the receipt of Applicant’s restriction election filed December 16, 2025. Applicant elects Group I, encompassing claims 1-5, 7-9, 57, 59, and 60. Because no traverse is presented, this election is treated as election without traverse. Groups 2 and 3 are pending. Groups 2 and 3 are withdrawn from examination. Group 1, claims 1-5, 7-9, 57, 59, and 60 drawn to a method of producing a doubled haploid plant comprising providing a plant comprising an introduced genetic chromosome doubling polypeptide and crossing with a second plant, wherein the polypeptide induces chromosome doubling of an egg cell are examined in the instant application.
The restriction is made FINAL .
Claim Status
Claims 11-14, 18-21, and 30-33 are newly canceled.
Claims 1-5, 7-9, 15-17, 22, 57, 59, and 60 are pending.
Claims 15-17 and 22 are withdrawn as a result of Restriction Requirement.
Claims 1-5, 7-9, 57, 59, and 60 are currently amended.
Claims 1-5, 7-9, 57, 59, and 60 are examined on the merits.
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.
Claim 60 is rejected as indefinite for the recitation “the second plant is a non-hybrid” The specification does not give objective boundaries of the term “non-hybrid”. The term “non-hybrid” is ambiguous and lacks clear boundaries, as it may refer to a non-F1 hybrid, an open-pollinated cultivar, an inbred line, or other breeding classifications. The claim does not specify which meaning is intended or provide objective criteria for determining whether a crop species qualifies as “non-hybrid”. Therefore, the metes and bounds of the claim are not reasonably certain.
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 1-5, 7-9, 57, 59, and 60 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.
Claims 1 and the dependent claims 2-5, 7- 9, 57, and 59-60 regards the “amino acid sequence having at least 90% identity to SEQ ID NO:23”, a genetic chromosome doubling polypeptide. SEQ ID NO:23 is ZM-CYCD2-related polypeptide, a maize cyclin delta-2-like protein (paragraph 0184). The claimed method requires the ZM-CYCD2-related polypeptide to endow the functional property of inducing chromosome doubling of an egg cell of a second plant when crossed.
The scope of the claimed genetic chromosome doubling polypeptide is broad, because it encompasses any polypeptide having at least 90% amino acid sequence identity to maize cyclin delta-2-like protein (SEQ ID NO:23).
In contrast to the broad scope, the Specification has described the cyclin gene-based genetic chromosome doubling factor, ZM-CYCD2 (DNA SEQ ID NO:17) encoding the cyclin delta-2-linke protein (protein SEQ ID NO:23), implemented in transformed haploid inducer lines as an introduced genetic chromosome doubling factor involving ZM-CYCD2 and/or limited variants thereof as having chromosome-doubling activity. For example, the specification describes that genetic chromosome doubling of a parthenogenic haploid embryos is achieved by providing to an egg cell the activity of a cyclin gene dpzm07g031470.1.1 encoding a cyclin delta-2-like protein, wherein activity during female gametogenesis provides chromosome doubling in vivo to yield a diploidized embryo comprising only maternal chromosomes (example 4C, paragraph 0184-0185) demonstrating introduction of egg-cell chromosome doubling and production of doubled haploid plant.
However, the Specification has not described other polypeptides within the broadly claimed ≥90% identity genus of ZM-CYCD2 related sequences as having the function of inducing chromosome doubling of an egg cell, as required by the claimed method. Nor has the specification described how sequence variation withing the claimed identity range affects, preserves, or abolishes the chromosome doubling function.
The Specification fails to sufficiently describe the necessary structural features that must be retained by ZM-CYCD2 related polypeptides to establish a structure-function relationship with respect to the specific function of inducing the egg cell chromosome doubling.
Firstly, the Specification has not described the essential structural features that must be shared by the members of the broad genus of ≥90% identity ZM-CYCD2 related polypeptides to achieve chromosome-doubling activity. Although cyclin D proteins share common cyclin domains, closely related cyclin D family members and variants are known to differ in regulatory roles, expression patterns, and biological function. The specification does not identify which structural features of ZM-CYCD2 proteins are responsible for the claimed chromosome-doubling activity. For example, Menges (Margit Menges et. al., Plant Physiology, Vol. 145, pp. 1558–1576, 2007) reports that Arabidopsis has 10 CYCD genes in seven subgroups, and discusses conservation/diversification across higher plants (page 1558). Godinez-Palma (Silvia K. Godínez-Palma, et. al., Journal of Experimental Botany, Vol. 64, No. 18, pp. 5661–5671, 2013) states “maize cells contain 17 different genes coding for D-type cyclins” maize has very close D2-type paralogs, Godinez-Palma notes cycD2:2 (a or b) are ~94% identical, yet still treated as distinct gene products/variants in maize (page 5562). Cyclin D proteins, including maize cyclin delta-2-like protein, are known cell-cycle regulators whose biological activity depends on precise interactions with CDKs and other regulatory factors, Godinez-Palma (page 5661) discloses “Binding to cyclin D2;2 was detectable at all germination times, forming a complex with kinase activity”. Cyclin-D function is not defined merely by overall “cyclin-like” similarity; rather, specific interaction determinants (such as the LxCxE-type pocket-protein interaction motif) can be required for RBR interaction, illustration the limited sequence change can disrupt key functional interactions even when overall identity remain high, Horvath (Beatrix M Horvath, et. al., 2;36(9):1261-1278, 2017) (page 1261 and 1273). Sabelli (Paolo A. Sabelli et. al., PNAS vol. 102 no. 37, pp13005-13012, 2005) discloses maize RBR family interaction networks shows that mutagenesis abolishes interactions, their data indicates interactions abolished by mutation of LxCxE motif, illustrating that LxCxE motif can be determinative for binding/function in RBR-linked cell-cycle regulation (page 13005, 13009). Boniotti (M B Boniotti et. al., Plant Journal, 28(3):341-350, 2001) also support that CDK/cyclin complexes bind and phosphorylate plant RBR proteins across species (maize included), reinforcing that RBR-axis interactions are central and thus structural determinants of those interactions’ mater (page 341, summary).
Secondly, the Specification has not described how the unspecified amino acid substitutions, deletions, or insertions withing the ≥90% identity range would impact the function of ZM-CYCD2-related protein. Such sequence changes may reduce, abolish, or otherwise alter cyclin-dependent kinase interactions or regulatory specificity, thereby affecting cell-cycle control and developmental outcomes. Without disclosure addressing how such variations affect function. It is unclear which embers of the claimed genus would retain the claimed chromosome-doubling activity. A study on leaf-petal allometry in Arabidopsis fine-mapped shows that CYCD2;1 varies in nature and is connected to G1 control/cell division rate: among the genes studied, a unique variant of the CYCD2;1 gene, which regulates the pace of cell division in the growth zones of the plant (meristems), was found exclusively in the Hi-0 strain of Arabidopsis. This unique gene variant is a likely reason why Hi-0 shows distinct growth characteristics (such as leaf/petal size or shape) Li(Xin Li, et. al., BMC Plant Biology, 20:547, pp1-11, 2020) (page 6). Multiple plant papers report that the same gene expressing CYCD2:1 cDNA can yield an aberrantly spliced mRNA that lacks part of the conserved cyclin box, and confirmed the cyclin box is essential for CDKA binding and gene function. Sanz (Luis Sanz et. al., Plant Cell. 23(2):641–660, 2011) (page 647). Therefore, Applicants have not adequately described the structural features that are required to be retained by members of the claimed genus as to establish a structure-function relationship, or the structural features required to distinguish members of the claimed genus from others.
The analysis will now turn to the second element of the court’s decision in Eli Lilly; namely, the description of a representative number of species within the claimed genus.
The broad genus of genetic chromosome doubling polypeptides defined by ≥90% sequence identity to maize cyclin delta-2-like protein (SEQ IC NO:23) is enormous in size. Allowing up to 10% sequence divergence across the ZM-CYCD2 polypeptide permits a very large number of distinct amino acid sequences, many of which may differ significantly in biological activity, including their ability to induce egg-cell chromosome doubling.
With regard to the ZM-CYCD2 gene with the wild-type cDNA sequence set forth in SEQ ID NO:17, the genus of variants encompassed by the claims is still enormous in size. For example, the cDNA of wild type ZM-CYCD2 gene has 1068 nucleotides. Even a single nucleotide substitution at any of the 1068 position would lead to at least 31068 possible variants. Even if the analysis is limited only to single-nucleotide substitutions, the number of potential variants is extremely large. The protein encoded by ZM-CYCD2 has 355 amino acids (SEQ ID NO:23). A single amino acid substitution at any of the 355 positions to any of the other 19 amino acids would result in at least 19428 possible variants.
Given the virtually infinite structural variable associated with these embodiments, the claims read on an extremely broad and highly diverse structures. Thus, in view of the analysis presented above, a skilled artisan would appreciate that the claims are directed to extremely broad and highly diverge genus of an amino acid sequence having at least 90% identity to SEQ ID NO:23 that are required to have the specific function of inducing chromosome doubling of an egg cell of a second plant when crossed.
In contrast, Applicant has only appeared to describe and reduce to practice only one specific polypeptide species, such as maize cyclin delta-2-like protein (SEQ IC NO:23) and no additional ≥90% identity variants of SEQ ID NO:23, for which chromosome-doubling activity has been demonstrated.
Given the large size and structural diversity associated with the claimed genus, Applicant’s disclosure is not representative of the claimed genus as a whole. This point is particularly relevant because, as discussed above, the prior art speaks to the disconnection between the structure of the broadly claimed variants and the recited specific function.
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. The specification does not reasonably convey to a person of ordinary skill in the art that applicant is in possession of the full scope of the claimed genus of ZM-CYCD2 -related polypeptides, including polypeptides having at least 90% identity to SEQ IC NO:23 that are capable of inducing egg-cell chromosome doubling, at the time this application was filed.
Scope of Enablement
Claims 1-5, 7-9, 57, 59, and 60 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specifications, while being enabling for maize maternal haploid induction using MTL/MATL haploid inducer lines transformed to express doubling factor ZmCYCD2 (SEQ ID NO:23); does not reasonably provide enablement for the full scope of the claimed method, including use of a genetic chromosome doubling polypeptide having at least 80% sequence identity to SEQ ID NO:23 in crosses where the first plant is of a different species or genera than the second plants. 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/or 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 1 and the dependent claims 2-5, 7- 9, 57, and 59-60 regards the “amino acid sequence having at least 90% identity to SEQ ID NO:23”, a genetic chromosome doubling polypeptide. Claims 57 regards the “first plant is a haploid inducer of a different species or genera than the second plant”.
Here, the claims recite a method requiring a first maize plant comprising a broad genus of genetic chromosome doubling polypeptide. The claimed method requires the genetic chromosome doubling polypeptide to endow a property of inducing chromosome doubling of an egg cell of the second plant in the absence of an exogenously applied chemical or biochemical chromosome doubling agent, and obtaining a diploidized embryo comprising a pair of chromosomes inherited from the second plant and not comprising the introduced genetic chromosome doubling polypeptide, followed by regeneration of a doubled haploid platelet or plant.
The scope of the broad genus of genetic chromosome doubling polypeptide is broad, because it encompasses any polypeptide having at least ≥90% sequence identity to SEQ ID NO:23, and the polypeptide is capable of performing the specific functional requirement recited in the claims (i.e., inducing chromosome doubling of an egg cell in vivo in the claimed crossing context, without chemical doubling gents).
Firstly, even when limited to plants, each species of plant has multiple cyclin genes that could be characterized as cyclin D (CYCD) family genes. For example, Arabidopsis has 10 CYCD genes in seven subgroups (page 1558). Menges also identifies 22 CYCD genes in poplar (Populus trichocarpa) genome (page 1558) and 14 CYCD genes in rice genome which fall into six or seven subgroups (page 1559). Godinez-Palma reports “maize cells contain 17 different genes coding for D-type cyclins”, Godinez-Palma mentions maize also has very close D2-type paralogs, cycD2:2 (a) and cycD2:2 (b) are ~94% identical, yet still treated as distinct gene products/variants in maize (page 5562).
Secondly, the claimed genus defined by “at least 90% identity to SEQ ID NO:23” encompass an enormous number of structurally distinct polypeptides. SEQ ID NO:23 is 355 amino acids in length. A 90% identity threshold permits up to approximately 35 amino acid differences relative to SEQ ID NO:23. Even limiting the analysis to substitutions (and not insertions/deletions). The number of possible sequence variants within that permitted sequence space is extremely large (i. e., substitutions at many combinations of positions, each with multiple alternative residues). Accordingly, the claimed genus encompasses a large number of structurally distinct polypeptides, each required by the claim to satisfy the same highly specific biological function in the context of the in vivo egg-cell chromosome doubling. For example, a mutation could also change the function of a gene. A study analyzing leaf-petal allometry in Arabidopsis identified natural variations in the cell division regulator CYCD2;1 as potentially responsible for distinct growth traits, including leaf and petal characteristics. A unique variant of this gene was found exclusively in the Hi-0 strain (Li, page 6).
In contrast to the broad scope, the Specification has provided enabling guidance for ZM-CYCD2 (DNA SEQID NO:17) encoding SEQ ID NO:23, wherein activity during female gametogenesis provided chromosome doubling activity in vivo to create a diploidized embryo having only maternal chromosomes (paragraph 0172-0192). The specification further provides illustrative plasmid/cassette contexts in which ZM-CYCD2 is placed under particular promoters/regulatory elements for delivery via pollen or early zygotic expression (e. g., plasmids listing ZM-CYCD2 as the doubling factor in tables describing transformation constructs and methods for generating transformed haploid inducer lines and performing haploid induction crosses) (example 1- 4).
However, the Specification has not provided enabling guidance for the full scope of the claimed genus of polypeptides having at least 90% identity to SEQ ID NO:23 to have the required function of inducing chromosome doubling of an egg cell in vivo, in the claimed crossing context, and yielding a diploidized embryo that lacks the introduced polypeptide. In particular, the specification does not teach which of the many permitted SEQ ID NO:23-like variants (including those with up to ~35 amino acid difference) will retain the required chromosome-doubling activity, under what expression timing/location, and in what plant genetic backgrounds, such that the claimed results is achieved without chemical doubling.
It is unpredictable how the broadly claimed sequence variants within the ≥90% identity genus would affect the required chromosome-doubling function. Cyclin proteins are cell-cycle regulators whose activity depends on precise structural determinants and interaction capabilities (Godinez-Palma, page 5661) (e. g., interaction with partner proteins and pathway components, appropriate expression timing, and effective activity in the relevant cell type). Thus, sequence variation permitted by the claims can alter the functional properties relevant to the claimed outcome, including whether the protein will produce the specific biological effect of egg-cell chromosome doubling in vivo, rather than other cell-cycle perturbations (e.g., altered division arrest, abnormal development, infertility, or lethality). In this case, the claims impose a highly specific functional requirement (egg-cell chromosome doubling producing a diploidized embryo with only maternal chromosomes, without chemical doubling agents), yet the specification does not provide guidance that correlates the broad identity-based sequence space to that specific function.
The unpredictability is further amplified by claim 57, which requires that the first plant is a haploid inducer of a different plant species or genera than the second plant. Under this limitation, the claims encompass wide-cross contests in which expression timing, compatibility, genome elimination dynamics, and cell-cycle regulation may differ substantially across species/genera. Plant hybridization is possible between close species but faces severe barriers, like hybrid lethality, sterility, and genetic incompatibility. Intergeneric ones are rare, often requiring specialized breeding to overcome embryo failure He (Hai He et. al., Frontiers in Plant Science, pp1-17, 2023) (page 1, abstract). He points reproductive isolation is also an obstacle to distant hybridization breeding in plants. “Reproductive isolation involves various pre-mating, post-mating prezygotic, and postzygotic isolating barriers in plants. Ecogeographic isolation and pollinator isolation are typical examples of pre mating isolation barriers, whereas interspecific pollen-pistil incompatibility, conspecific pollen precedence, gametic incompatibility, and pistil length mismatch are examples of post-mating prezygotic isolating barriers. Postzygotic isolation barriers include hybrid seed lethality, immature fruit abscission, hybrid seedling lethality or unviability, hybrid weakness, hybrid sterility, and hybrid breakdown” (page 2). He (fig 1) also discussed the Bateson–Dobzhansky–Muller model explains that interactions of genes from different parents can cause failure. The specification’s disclosure focused on specific illustrative embodiments does not provide sufficient enabling teachings for how to select, modify, and validate the many SEQ ID NO:23-like variants across the wide range of species/genera and crossing contexts encompassed by the claims, while still achieving the claimed diploidized embryo outcome.
With regard to the above discussed unpredictability, neither the instant application nor the prior art cited in the specification provides sufficient teachings to overcome the deficiency for the entire claimed genus. Applicant has provided working guidance for the specific ZM-CYCD2 embodiment (SEQ ID NO:23 as encoded by SEQ ID NO:17) in particular construct/promoter contexts and within the described haploid induction framework. But the specification does not provide commensurate enabling guidance for the full breadth of SEQ ID NO:23-like variants permitted by the ≥90% identity definition, nor for carrying out the claimed method across the broad range of interspecific/intergeneric contests encompassed by claim 57.
Thus, in view of the unpredictability associated with cyclin-mediated cell-cycle perturbation in vivo, the unpredictability of how sequence variation with the ≥90% identity genus impacts the required egg-cell chromosome-doubling function, the lack of enabling guidance from either the instant disclosure or the art, and breath and diversity of the embodiments encompassed by the claimed genus, the lack of sufficient working examples, and the level of the art at the time of the invention, one of ordinary skill in the art must rely on undue trial and error experimentation to make and test the numerous genes having unspecified mutations, in order to make and/or use the invention commensurate to the full scope of these Claims.
For at least this reason, the Specification does not teach a person with skill in the art how to make and/or use the subject matter within the full scope of these Claims without undue experimentation.
Conclusion
No claims are allowed.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663