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 .
Claim Status
Claims 1, 5-6, 29 and 31-33 remain pending.
Claim 1 is newly amended.
Claims 1, 5-6, 29 and 31-33 remain rejected.
Response to Applicant’s Arguments – Objections to the Specification
In response to Applicant’s arguments and amendments to the specification dated 02/17/2026, the objections to the specification of record are withdrawn.
Response to Applicant’s Arguments – 35 USC § 112 (Indefiniteness)
In response to Applicant’s arguments and amendments to the claims dated 02/17/2026, the indefiniteness rejections of record are withdrawn.
Response to Arguments – Written Description
Applicant’s arguments and amendments dated 02/17/2026 have been fully considered but are not found to be persuasive and the rejections of record are maintained. Applicant’s arguments are summarized and addressed below.
Applicant’s arguments are drawn to the following theme:
The claims have been amended to recite that the PP2Cs ABI1, ABI2 and HAI2 are each silenced. The specification provides description of apomixis/sex switching which is regulated by manipulating defined signaling pathways. Some reports support the theory that enhancing stress attenuation in sexual plants suppresses meiosis and induces apomeiosis. Finally, the abscisic acid pathway including PP2Cs enhances stress attenuation. Therefore, applicant’s independent claim drawn to inducing apomixis by silencing the three PP2Cs and increasing stress has been adequately described.
This argument is not found to be persuasive because applicant has simply described general expression patterns found to differ in apomictic and sexually reproducing plants and suggested that decreasing the expression of one of several targets will confer the claimed phenotype of induced gametophytic apomixis without any demonstration that the targeting of these genes with silencing can produce apomixis.
Even five years after the filing of this application the mechanism underlying apomixis remains unclear. To illustrate see the following excerpt from the Abstract of Niccolo (Nicollo, Planta, 2023).
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In this section of the abstract Niccolo makes clear the following points which are germane to the written description rejections of record. First, Niccolo states unequivocally that the genetic basis, origins and mechanisms of apomixis are unclear. Second, Niccolo presents three central hypotheses for the development of apomixis, however none of these hypotheses specifically present stress as the central regulator of apomixis nor the ABA signaling pathway as the apomixis switch. To reiterate, five years after the instant application there is no clear understanding of the mechanism underlying apomixis in plants. Further, at this time it does not appear that the mechanism proposed by applicant was considered among the most likely hypotheses for the development/origin/mechanism of apomixis.
Therefore, currently applicant’s disclosure acts more as an invitation to experimentation than a demonstration that the applicant was in possession of the claimed invention, leaving at least the following questions:
To what degree must target gene expression be decreased in order to produce the claimed phenotype and does this change based on target gene, target plant or any other parameter.
Must this targeting and potential resultant increase in SnRK2 activity occur at a specific developmental timepoint in order to produce the claimed phenotype.
Without the answers to at least these questions or any other evidence which produces a structure function relationship between the targeting of ABI1, ABI2, AIP1 in any member of the Brassicaceae, Fabaceae or Poaceae and the induction of gametophytic apomixis in these species it is not possible for the ordinary artisan to determine if any silencing approach taken at any developmental time point which targets any one of the claimed target genes in any plant from the Brassicaceae, Fabaceae or Poaceae regardless of genetic background would produce the claimed phenotype of inducing gametophytic apomixis in a sexual angiosperm.
Additionally the state of the art appears to teach away from the claimed methods. For example, Lim discloses SnRK2 mutants and there is no link to apomixis in this disclosure (Lim, Environmental and Experimental Botany 212 (2023)). Lim also discusses HAI (AIP) knockout mutants which produced delayed seed germination without any discussion of apomixis (Lim, Page 3, Column 2, Only Paragraph). In fact, Sherwood, in work cited by and incorporated in its entirety by the instant disclosure, states in the abstract that “apomixis is not a mutationally derived condition caused by “broken genes”, but rather an alternative mode of reproduction anciently embedded in the genomes of angiosperms that can be triggered by the appropriate metabolic signals” (Sherwood, Page iv, Final Sentence).
This teaches against applicant’s claimed invention which is essentially a method of breaking one of three target genes and their orthologs by preventing their expression using gene silencing to target them. Further, applicant fails to provide details or description of the metabolic signals which are required for the switch Sherwood describes.
Despite applicants urging that the scope of the claim is commensurate with the description provided in the specification in light of the state of the art, it does not appear that applicant was in possession of the claimed invention at the time of filing and therefore applicants arguments are not found to be persuasive and the written description rejections of record are maintained.
Written Description
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.
This rejection is maintained for the reasons of record, because the amendments and remarks by Applicants in response to Office Action mailed on November 17, 2025, have been fully considered but not deemed persuasive, see above.
Claims 1, 5-6, 29 and 31-33 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 pre-AIA 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 drawn to a method of inducing gametophytic apomixis in a sexual angiosperm by introducing silencing elements which target polynucleotides encoding the following group C protein phosphatase 2C proteins: abscisic acid insensitive 1 (ABI1), abscisic acid insensitive 2 (ABI2) and highly ABA-induced PP2C 2 (HAI2).
The broadest reasonable interpretation of the claim includes scope where the three claimed genes are broken by preventing their expression which then modulates SnRK2 activity which results in a sexual angiosperm from the Brassicaceae, Fabaceae or Poaceae, switching from sexual reproduction to apomictic reproduction.
In providing their description of the claimed invention applicant has described known stress pathways but does not appear to have added anything that demonstrates that gene silencing of the target genes produces the claimed induced apomixis phenotype.
From the disclosure and the state of the art with respect to stress signaling and apomixis applicant’s disclosure appears to have the following flaws:
Applicant has claimed a method of metabolic switching between apomixis and sexual reproduction in a eukaryote which appears to be an implicit property of plants.
The disclosure is missing something, specifically what exactly has to happen in order to lead to switching from sexual reproduction to apomixis in any plant (Emphasis added).
With respect to 1. above, evidence that metabolic switching in response to different stress conditions in plants is an inherent and natural property is presented in the instant disclosure including in applicant remarks dated 06/12/2025.
Specifically, Applicant urges that “ovules of apomictic plants maintain higher levels of metabolic homeostasis for stress attenuation, which suppress meiosis and induce apomeiosis” and then further states that “it is well-established that ABA accumulates in response to stress, binds to PYR/PYL?RCAR receptors, and inhibits clade A PP2Cs such as ABI1, ABI2, and AIP1” and that “the ABA-PYL receptor complex subsequently inhibits downstream protein phosphatases in clade A of the PP2C family. Id. PP2C inhibition releases sucrose non-fermenting-1 (SNF1) related protein kinase-2s (SnRK2s), which phosphorylate downstream effectors to initiate protective responses such as stomatal closure and gene expression reprogramming” (Remarks, Pages 6-7, Third Full Paragraph on Page 6 to First Paragraph on Page 7).
However, despite these assertions, applicant does not provide a concrete mechanism which links reduced expression of the claimed genes, including by gene silencing approaches, to apomixis. Instead, Applicant presents reduced class A PP2C expression as an inherent characteristic of the switch from sexual to apomictic reproduction and therefore, applicant’s claimed method of metabolic switching appears to be a natural phenomenon.
Further evidence of this can be found in the conclusion of Sherwood; “Since stress signaling is responsible for triggering meiosis and the formation of reduced gametes (Chapter 3), it appears from the present study that it might weave together these two steps to form sexual reproduction…These results provide an evolutionarily parsimonious explanation for the repeated occurrence of apomixis in plants and animals…My research provides compelling evidence that apomixis may have been embedded early into eukaryotic evolution as a default reproductive program in growth favoring environments with stress signaling triggering the alternative, i.e. sexual reproduction” (Sherwood, Page 86, First Full Paragraph)( Sherwood, Diss. Utah State University, 2018).
The introduction of Sherwood also indicates that the induction of apomixis in sexual plants is naturally occurring stating that “apomixis is not a mutationally derived condition caused by “broken genes”, but rather an alternative mode of reproduction anciently imbedded in the genomes of angiosperms that can be triggered by the appropriate metabolic signals” (Sherwood, Page iv, Last sentence).
As such it appears that this switch to apomixis by reduced expression of the claimed genes may be a natural phenomenon. It is not clear how applicant’s claimed method differs from the naturally occurring mechanism and therefore, it is not clear how the ordinary artisan would be able to determine if a plant having switched from sexual to apomictic reproduction had underwent the claimed method or instead if increased and naturally occurring stress lead to the activation of the intrinsic switching mechanism which resulted in the switch in reproductive strategy. The answer to this question may provide clarity on the description required in order to demonstrate possession of the claimed methods.
Alternatively, if this switching is not a natural and inherent property of plants then as described in 2. above, applicant’s disclosure is missing some description that is required in order for the method of reducing the expression of the target genes to lead to the induction of apomixis in sexually reproducing plants.
This is because a review of the instant disclosure reveals no description which links reduced expression of the claimed target genes to the induction of apomixis in all members of the Brassicaceae, Fabaceae and Poaceae and there is no example, reduced to practice, which demonstrates that targeting these genes with silencing approaches produces induced apomixis.
A review of the prior art reveals that PP2C interaction with and regulation of SnRK2s was known in the art but there is no evidence to demonstrate that reduced expression of PP2Cs leads directly to induced apomixis in all of the claimed plants. For example, Lim discloses SnRK2 mutants but does not describe any link between these mutants and apomixis (Lim, Environmental and Experimental Botany 212 (2023)). Lim also discusses HAI (AIP) knockout mutants which produced delayed seed germination and even in this section drawn to reproduction and seed characteristics there was no discussion of apomixis (Lim, Page 3, Column 2, Only Paragraph).
In fact, Sherwood, which was cited by and incorporated in its entirety by the instant disclosure, states in that “apomixis is not a mutationally derived condition caused by “broken genes”, but rather an alternative mode of reproduction anciently embedded in the genomes of angiosperms that can be triggered by the appropriate metabolic signals” (Sherwood, Page iv, Final Sentence). This is another teaching away from applicant’s claimed invention which is essentially method of breaking three target genes by preventing their expression using gene silencing to target them.
Further, the complexity of inducing this shift is also made clear by Sherwood; “The low frequency of inducing parthenogenesis in the present study may be due to the difficulty of the glucose BR solution diffusing through many cell layers (thicker pistil wall and ovules walls) to reach the CC and egg. As a next step, genetic engineering may enable cell or tissue specific activation of the glucose-TOR and BR signaling pathways to induce high frequency parthenogenesis in otherwise obligately sexual crops” (Sherwood, Page 86, Second Paragraph).
Sherwood is a particularly helpful reference because it makes clear the two aspects of applicant’s disclosure that lead to issues with written description.
First, Sherwood states clearly that apomixis appears to be an evolutionarily derived intrinsic characteristic of plants which is not simply a product of recently broken genes. Secondly Sherwood, describes the complexity of the shift from sexual to apomictic reproduction, proposing putative solutions to low frequencies or inability to induce apomixis in sexual crops.
Taken together Sherwood states that the shift to apomixis is a naturally occurring complex shift which is challenging to induce even at low frequencies and with the use of carefully delivered chemicals.
As such the two questions presented above remain.
If apomixis is naturally occurring in plants how would the ordinary artisan identify if they were in possession of the claimed method? How could they tell if the plant went through the natural process to induce apomixis or if instead it was the interventions described in the claims that lead to apomixis?
Given the complexity of the mechanism underlying the switch from sexual to apomictic reproduction what specifically must be done in order to induce apomixis in all of the claimed plants? Is any method which reduces the expression of the claimed genes by any amount sufficient to induce apomixis? If not what level of reduced expression is required? Must this reduced expression happen at a certain time point? How do the required steps/conditions interact with Lim which did not report induction of apomixis upon knockout mutation of PP2Cs including HAI genes?
Given that the answers to these questions are unclear given the description found in the instant disclosure and the state of the art and given the analysis above, it appears that 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. As a result, it does not appear that Applicant was in possession of the claimed invention at the time this application was filed and claims 1, 5-6, 29 and 31-33 remain rejected as lacking adequate written description.
Conclusion
Claims 1, 5-6, 29 and 31-33 remain rejected.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached on 7:30 to 5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
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