DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1, 4-16, 18, 21-22, 24-27, 33, 36 & 38-42 are under examination on the merits.
The objections to claims 1, 12, 14, 24 & 33 are withdrawn in light of Applicant’s amendments.
The rejections of claims 33, 36 & 37 under 35 U.S.C. 101 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 under 35 U.S.C. 112(a) for written description is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 under 35 U.S.C. 112(a) for scope of enablement is withdrawn in light of Applicant’s amendments.
The rejection of claim(s) 37 under 35 U.S.C. 102(a)(1) as being anticipated by Hammoudi et al (2016) New Phytologist. 211: 172-185 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, 34, & 37-42 under 35 U.S.C. 103 as being unpatentable over Takeda et al (2004) Genes & Development. 18:782–793, hereafter Takeda, taken with the evidence of GenBank accession number AY560347 is withdrawn in light of Applicant’s amendments.
Claim Objections
Claim 33 is objected to because of the following informalities:
Claim 33 (line 3): “at least one the plant” should read --the plant-- in keeping with the claim amendments filed 10/21/2025 and not marked up in the claimset filed 7/14/2026.
Claim 33 (line 15): a conjunction like “and” is needed before the last “wherein” clause.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 27, 33, 36, 41 & 42 are 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. All dependent claims are included in the rejections below.
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 4/6/2026, as applied to claim 27. Applicant' s arguments filed 7/14/2026 have been fully considered but they are not persuasive.
Claim 27 recites repeating steps (iv) and (v), wherein step (iv) is followed by step (v). These steps comprise growing “the” plant to seed and growing the seeds obtained in step iv to a plant. “The” plant has antecedent basis in the plant comprising increased tandem duplication (claim 1, step ii). Thus, claim 27 appears to require growing the same plant to seed, twice. However, the example of Arabidopsis in the instant specification (example 1, page 38, and example 4, page 40) and claim 24 encompass annual, determinate species that grow to seed once. It is unclear if 27 is strictly limited to a method of repeating steps (iv) and (v) and growing “the plant” to seed twice, or if claim 27 encompasses methods wherein the plants of the seeds of step (v) are grown to seed.
Claim 33 recites “the wildtype plant” in line 15. There is insufficient antecedent basis for this limitation in the claim. No wildtype plant has been established in the claim, and it is unclear whether the “wildtype” plant is in reference to a TONSOKU nucleic acid sequence only or with respect to other genes. Dependent claims 36, 41 & 42 are also indefinite.
Applicant urges that amended claim 27 clarifies that the steps are repeated in the order of (iv) -> (v) -> (iv) -> (v) (Remarks page 8, paragraph 7-page 9, paragraph 2).
This argument is unpersuasive, because the amended claim still encompasses methods wherein the original plant is grown to seed more than once. Step (iv) would be followed by step (v) in both interpretations presented in the rejection above. If the claim is intended to encompass only methods wherein the plant grown from obtained seed(s) in step (v) is subsequently grown to seed, wording regarding repeating the steps over additional generations might help to clarify the interpretation of the claim.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, & 38-42 are rejected under 35 U.S.C. 103 as being unpatentable over Takeda et al (2004) Genes & Development. 18:782–793, hereafter Takeda, taken with the evidence of GenBank accession number AY560347 (available online 4/13/2004).
This is a new rejection from the rejection mailed 4/6/2026. Applicant' s arguments filed 7/14/2026 have been fully considered below as they apply to the current rejection but they are not persuasive.
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, & 38-42 are drawn to a method of generating a plant with a trait of interest by reducing or abolishing the level of a TONSOKU polypeptide in a population of plants, as well as a plant obtained by this method.
Takeda teaches Arabidopsis mutants in the BRUSHY1 gene generated by T-DNA random insertion mutagenesis (page 783, right column, paragraph 3). The instant specification describes BRUSHY1 as the same gene as TONSOKU (page 8, paragraph 4). Takeda teaches a method of screening the mutant plants for traits of interest, namely sensitivity to methane sulfonate (page 783, right column, paragraph 3). The method of screening involved growing the plants (page 790, right column, final paragraph). Takeda teaches multiple alleles, and describes the two mutants with less severe phenotypes as partial loss of function mutants (page 784, left column, paragraph 2). Takeda teaches the mutations as recessive (page 783, right column, paragraph 3).
Takeda identifies the gene involved as encoding an amino acid sequence with the sequence of GenBank accession no. AY560347 (page 784, right column, second paragraph). AY560347 has 100% sequence homology to instant SEQ ID NO: 1; see alignment above.
Takeda teaches mutations in the gene as a deletion, a substitution, and an insertion in the gene (page 784, right column, third paragraph-page 785, left column, paragraph 1; figure 3B). Takeda teaches that bru1-1 mutants exhibit epistasis with fas1-1 and fas2-2 mutants based on double mutant lines (page 788, left column, paragraph 4). Takeda teaches that expression of BRU1 is detectable in suspension culture cells (page 785, left column, paragraph 2).
Takeda teaches that mutations in BRU1 lead to fourfold higher rates of homologous recombination (page 785, right column, paragraph 1). Takeda teaches that mutations in BRU1 had less transcriptional gene silencing (page 786, left column paragraph 2). Takeda teaches a method for testing homologous recombination wherein a heterozygous bru1-1 mutant was crossed with a plant comprising a recombination trap, an F2 generation was created, and progeny was genotyped for homozygous bru1-1 mutants (page 786, figure 4 caption).
Takeda does not teach the sequence of BRU1 directly but identifies the gene as At3g18730 and GenBank accession number AY560347 (page 784, right column, paragraph 2).
Takeda is silent as to whether the plants with reduced or abolished expression of a TONSOKU nucleic acid sequence have increased tandem duplication.
Before the filing of the instant application, the method of identifying a plant comprising increased tandem duplication, comprising identifying or selecting at least one plant comprised increased tandem duplication and growing the plant to form a population of plants (instant claim 33) would have been obvious over Takeda, because Takeda identified plants with a trait of interest (sensitivity to methane sulfonate) and crossed these plants. The instant specification describes de novo tandem duplication events to occur at a rate of 7 per generation; no Arabidopsis lines had 0 tandem duplications in a generation (figure 3, page 40, line 33-page 41 line 3). Because tandem duplications inherently result from the reduced activity, expression, or level of TONSOKU in an Arabidopsis plant, the Arabidopsis lines identified and selected by Takeda, which were TONSOKU-deficient, would comprise increased tandem duplications, even though Takeda is silent about this feature. The TONSOKU-deficient lines would have increased tandem duplication relative to lines without the mutation, which read on a wildtype plant. Therefore, the method of Takeda would make obvious the method of claims 33 prior to the filing of the instant application.
Likewise, claims 1 & 8-10 & 13-14 are drawn to the method of providing a population of plants comprising an endogenous TONSOKU nucleic acid, reducing or abolishing TONSOKU expression or activity in the population of plants to generate a plant comprising increased tandem duplication within the genome of the plant, and identifying or selecting a plant with increased tandem duplication. Although Takeda is silent about the presence or absence of tandem duplications in the genome of the TONSOKU mutant plants, these Arabidopsis lines of Takeda would inherently comprise tandem duplications at a level higher than plants without the TONSOKU mutation. The screening of plants for a trait of interest, as taught by Takeda, would make obvious a method wherein plants comprising increased tandem duplication were generated and indirectly selected by selection on another trait such as sensitivity to methane sulfonate. The plant of Takeda, which reads on a population of plant cells, comprises an insertion mutation in the TONSOKU gene (claims 8 & 10). The mutation was generated by a T-DNA insertion mutagenesis (claims 13-14). Plants were screened to identify those that were homozygous for the mutation (claim 15). Plants were assayed for sensitivity to methane sulfonate which reads on selecting the plant by assessing the behavior of at least one plant cell of the plant comprising increased tandem duplication in a phenotypic assay (claim 42).
Additionally, the method of Takeda comprising growing plants comprising the TONSOKU homolog mutation in order to make crosses up to at least the F2 generation (page 786, figure 4 caption) inherently involves growing a mutant plant to seed (claim 25) and growing the seeds obtained (claim 26), which would result in an F1 generation. Takeda’s method also reads on a method that comprises growing the plant comprising increased tandem duplication (claim 40) to seed to obtain progeny (claim 41).
Some, if not all, of the generated plants from reduced or abolished TONSOKU activity would inherently also comprise two tandem duplications (instant claim 4) or three tandem duplications (instant claim 5) and these tandem duplications would occur at random locations (instant claim 6) and comprise a repeated sequence of 50-500 Kb (instant claim 7), because de novo tandem duplication events at random locations in the genome inherently occur at a rate of 7 per generation in an Arabidopsis mutant for TONSOKU, and some of these random duplications will comprise repeated sequences of at least 50Kb (instant specification, figure 3, page 40, line 33-page 41 line 3).
The Arabidopsis mutant line taught by Takeda reads on a population. However, the instant specification defines a plant to encompass a plant cell (page 35, lines 1-5). Takeda teaches plant tissues and plant parts by provided pictures of the plants where leaves and floral structures are visible (figure 2), which read on a population of plant cells obtained from plant tissue (claim 21) and plant tissue comprising a plant part (claim 22), including where the plant tissue or plant part is leaves (claims 38-39).
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33 & 38-42 are obvious over Takeda.
Applicant urges that the cited prior art documents do not disclose identifying or selecting a plant on the basis of increased tandem duplication and the mechanism by which tandem duplications were formed was unknown, so tandem duplications being intentionally generated to introduce genetic variation was discovered by the instant inventors. Applicant urges that even if the TONSOKU mutants known in the art inherently included tandem duplications, there is no teaching linking TONSOKU function to tandem duplication or identifying plants based on this characteristic. Applicant urges that the instant invention stems from the recognition of a previously unrecognized relationship and deliberate selection of plants comprising increased tandem duplications (Remarks, page 12, paragraph 6-page 13, paragraph 1).
This argument is unpersuasive, because the instantly claimed methods do not require an active step wherein tandem duplications are identified, merely a step wherein a plant comprising tandem duplications is identified or selected. Because the art teaches that plants comprising TONSOKU mutations comprise identifiable phenotypes other than tandem duplications, methods of selecting plants that would inherently have increased tandem duplications relative to wildtype were known in the art prior to the instant filing.
The instant application describes an example of identifying de novo tandem duplications in a plant comprising whole-genome resequencing and detection of copy number variation (page 40, lines 19-31). However, the instant claims do not require any step of directly observing or identifying de novo tandem duplications in the genome of a plant. Thus, the silence in the prior art with respect to increased tandem duplication in TONSOKU mutant plants does not make the instant methods non-obvious. The motivation to perform the steps in a claimed method do not need to Applicant’s own motivation in order for the method to be obvious.
Claims 1, 4-15, 21, 22, 24-27, 33, 36, & 38-42 are rejected under 35 U.S.C. 103 as being unpatentable over Gherbi et al (2001) EMBO reports. 2(4):287–291 (published 4/1/2001, hereafter Gherbi); in view of Wright et al (2005) The Plant Journal 44:693–705 (published 10/18/2005 hereafter Wright); in further view of Takeda et al (2004) Genes & Development. 18:782–793 (published 2004, hereafter Takeda).
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 4/6/2026, as applied to claims 1, 4-15, 21, 22, 24-27, 33, 34, & 36-42. Applicant' s arguments filed 7/14/2026 have been fully considered but they are not persuasive.
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, & 38-42 are summarized above. Claim 9 requires a loss of function mutation. Claim 24 is drawn to a method of reducing or abolishing the level of a TONSOKU polypeptide in a plant selected from a list of plants. Claims 11-12 are drawn to a method of modifying a TONSOKU gene via targeted mutagenesis. Claim 36 is drawn to a method wherein identifying or selecting the plant comprising increased tandem duplication comprises screening for a trait of interest.
Gherbi teaches Arabidopsis mutants homozygous for a T-DNA insertion in the RAD50 gene (page 290, left column, paragraph 3) have increased homologous recombination, including gene conversion relative to heterozygotes (page 288, right column, paragraph 1-2 and figure 4). Gherbi teaches a method of crossing RAD50 mutants with GUS recombination tester lines and screening for a trait of interest (antibiotic resistance) in the F3 generation (page 290, left column, paragraph 3). Gherbi does teach genotyping the plants for zygosity of the mutation by PCR prior to screening for increased recombination (page 288, left column, paragraph 1, figure 2). Thus, Gherbi teaches a method of increasing genome modification in a plant cell by mutating the gene encoding a polypeptide.
Gherbi does not teach a TONSOKU protein or gene, nor a method of reducing the level of a TONSOKU protein in a plant cell, nor a plant created by the method of reducing the level of a TONSOKU protein. Gherbi does not teach introducing a mutation into a TONSOKU gene, nor a method of mutation involving targeted genome modification, nor a method to reduce protein levels involving RNA interference or an inhibitor. Gherbi does not teach an increase in tandem duplications due to the method. Gherbi does not teach the reduction of a TONSOKU gene in a population of cells and growing the cells into a plant. Gherbi does not teach the method in any of the plants listed in claim 24 nor the traits in claim 36.
Wright teaches a method to increase homologous recombination in tobacco by introducing a construct encoding a zinc-finger nuclease via leaf disk transformation (page703, right column, paragraphs 2-3). Wright teaches a motivation to increase homologous recombination in plants, in that homologous recombination can create precise deletions, insertions, or mutations and that plant chromosomal modification through homologous recombination “has been a long sought after goal of plant biology” (page 693, left column, paragraph 1). Wright teaches a method of introducing zinc-finger nucleases and donor DNA into plant cells (page 696, right column, second paragraph) to specifically mutate a reporter gene (page 695, left column, paragraph 3). Wright teaches a motivation to use targeted genome modification in plant to perform gene targeting of valuable traits like increased resistance to disease or stress or altered oil or carbohydrate profiles (page 693, right column, paragraph 1) while allowing for greater public acceptance than other transformation methods (page 703, left column, paragraph 3), as well as a motivation to use zinc-finger nucleases because they can recognize extended sequence patterns with great specificity and affinity (page 694, right column first paragraph). Wright teaches a method where shoot cultures are grown from transformed leaf disks and the expression of the target gene in T0 plants is verified with RT-PCR (page703, right column, paragraphs 3). Wright also teaches protoplast cultures derived from shoot cultures, transformed by electroporation, and regenerated into plants (page 703, right column, paragraphs 3- page 401, left column, first paragraph).
The teachings of Takeda are summarized above.
Before the date of filing of the instant application, it would have been obvious to one having ordinary skill in the art to modify the method taught by Gherbi to mutate a RAD50 gene to increase homologous recombination in a plant cell with the method of Takeda to reduce the level of a TONSOKU/BRUSHY1 polypeptide to increase homologous recombination. One would have been motivated to increase recombination in a plant cell because Wright taught that increasing homologous recombination in plants had long been a goal for mutating DNA sequences within native chromosomal contexts (page 693, left column, paragraph 1). Because mutations in both RAD50 (Gherbi, abstract) and TONSOKU/BRUSHY1 (Takeda abstract) had been known in the art to increase homologous recombination, one of ordinary skill in the art would have had reasonable expectation of success in mutating TONSOKU in increase homologous recombination.
Although Gherbi, Wright, and Takeda are silent with regard to the presence or absence of tandem duplications, or traits that result from tandem duplications, a plant with a reduced or abolished expression, activity, or level of TONSOKU would inherently have tandem duplications, as presented above.
Regarding claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33 & 38-42, the limitations of the claims are taught by Takeda, as summarized above.
Regarding claim 9, it would have been obvious before the time of filing from Takeda that a loss of function mutation would increase the homologous recombination phenotype observed, and Takeda indirectly suggests that bru1-3 is a loss of function mutation compared to the weaker phenotypes in the bru1-1 and bru1-2 mutants, hypothesized to be partial loss-of-function mutations (page 784, left column paragraph 2). Thus, in light of Takeda, a method of reducing the level of a TONSOKU polypeptide further comprising a mutation in a TONSOKU gene comprising a loss of function mutation would have been obvious at the time of filing.
Regarding claims 11-12, before the time of filing of the instant application, one of ordinary skill in the would have been motivated to modify the method taught by Gherbi/Takeda to reduce the level of a TONSOKU polypeptide by the method taught by Wright of targeted mutagenesis using zinc-finger nucleases. One of ordinary skill in the art would have been motivated to do so because zinc-finger nucleases for targeted mutagenesis allows for changing plant genomes in a specific and controlled manner, which could allow for greater public acceptance than other transformation methods and enables creating crops with valuable traits. One of ordinary skill in the art would have had reasonable expectation of success because zinc-finger nuclease mediated gene targeting had been widely used at the time of filing of the instant application.
Regarding claim 24, before the time of filing of the instant application, one of ordinary skill in the art would have found it obvious to use tobacco instead of Arabidopsis in the method of Gherbi because Wright taught a method to increase homologous recombination using tobacco plants and cell lines (abstract). One would have had reasonable confidence of success because a homolog of BRU1 was known in tobacco (Takeda, page 785, left column, paragraph 3). Thus, the method of claim 24 to reduce the level of a TONSOKU polypeptide in a plant cell in a tobacco plant would have been obvious at the time of filing of the instant application.
Regarding claim 27, claim 27 is drawn to a method comprising repeating steps (iv) and (v) of claims 25 and 26. Although the interpretation of claim 27 is indefinite, it could encompass methods wherein the seeds grown to a plant in step (v) are grown to seed to obtain additional plants in addition to a method of re-growing the plant from step (ii) of claim 1 to seed.
The first interpretation would be obvious over the TONSOKU mutant Arabidopsis lines of Takeda, because the maintenance of lines would encompass growing multiple generations to seed. With respect to the second interpretation, before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the method taught by Gherbi/Takeda to reduce the level of a TONSOKU polypeptide in a plant cell with the method taught by Wright to maintain transformed plants via aseptic shoot cultures. It would have been obvious before the time of filing to generate and maintain shoot cultures for a transgenic plant such as tobacco, because transformation methods such as leaf disk transformation involve regenerating plants in aseptic shoot cultures. Growing shoot cultures to seed and then growing the seeds obtained would have been obvious for experiments involving crossing of mutants with reporter lines (eg Gherbi). To repeat the process of growing the plant to seed and growing the seeds obtained, as recited in claim 27, would have likewise been obvious because more than one cross between TONSOKU mutants and other genetic lines was desired. Takeda made double mutant lines with two other genes to test interactions. Thus, before the time of filing of the instant application it would have been obvious to modify the method of Gherbi/Takeda with the method of Wright to maintain the original plant line in shoot culture in order to repeat the steps of growing the plant to seed and growing seeds. One of skill in the art would have been motivated to do so in order to cross the mutant line with other genetic lines. One of ordinary skill would have been reasonably confident of success because shoot culture methods were routine at the time of filing of the instant application.
Finally, it would have been obvious to one of ordinary skill in the art to modify the method to screen for a trait such as altered carbohydrate profiles or disease or stress resistance (instant claim 36) rather than or in addition to sensitivity to methane sulfonate. One of skill in the art would have been motivated to screen for these traits of interest, because Wright teaches that these are traits of high-value crops. One of ordinary skill in the art would have had reasonable expectation of success in screening for these traits, because methods of screening for plant traits was routine in the art prior to the filing of the instant application.
Claims 1, 4-15, 21, 22, 24-27, 33, 36, & 38-42 are obvious over Gherbi, Wright, and Takeda.
Applicant urges that the cited prior art documents do not disclose identifying or selecting a plant on the basis of increased tandem duplication and the mechanism by which tandem duplications were formed was unknown, so tandem duplications being intentionally generated to introduce genetic variation was discovered by the instant inventors. Applicant urges that the instant invention stems from the recognition of a previously unrecognized relationship and deliberate selection of plants comprising increased tandem duplications (Remarks, page 12, paragraph 6-page 13, paragraph 1).
This argument is unpersuasive, because the instantly claimed methods do not require an active step wherein tandem duplications are identified, merely a step wherein a plant comprising tandem duplications is identified or selected. Because the art teaches that plants comprising TONSOKU mutations comprise identifiable phenotypes other than tandem duplications, methods of selecting plants that would inherently have increased tandem duplications relative to wildtype were known in the art prior to the instant filing.
The instant claims do not require any step of directly observing or identifying de novo tandem duplications in the genome of a plant. The silence in the prior art with respect to increased tandem duplication in TONSOKU mutant plants does not make the instant methods non-obvious, because the motivation to perform the steps taught by the prior art do not need to Applicant’s own motivation in order for the method to be obvious.
Applicant urges that because the prior art documents do not disclose identifying or selecting a plant on the basis of increased tandem duplication or the mechanism by which tandem duplications are formed, there is no reason why a skilled person would combine the teachings of Gherbi, Wright, and Takeda (Remarks, page 13, paragraph 2).
This argument is unpersuasive, because the instantly claimed methods do not require an active step wherein tandem duplications are identified, merely a step wherein a plant comprising tandem duplications is identified or selected. The prior art suggests other phenotypes and motivations for selecting or identifying a plant with reduced TONSOKU, and such plants would inherently comprise increased tandem duplications, so methods comprising selecting or identifying TONSOKU mutant plants, which would inherently comprise increased tandem duplications, are obvious over methods known in the prior art. The motivation to perform the steps in a claimed method do not need to Applicant’s own motivation in order for the method to be obvious.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, as applied to claims 1, 4-15, 21, 22, 24-27, 33, 36, & 38-42 above, and further in view of Dubois et al (2011) PLoS One. 6(4), e18658.
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 4/6/2026, as applied to claims 1, 4-16, 21, 22, 24-27, 33, 34, & 36-42. Applicant' s arguments filed 7/14/2026 have been fully considered (see response to Applicant’s Remarks in the rejection above), but they are not persuasive.
Claim 16 is drawn to a method comprising using RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence.
The teachings of Gherbi, Wright, and Takeda are summarized above. Of emphasis, Takeda teaches that at least one mutant of a TONSOKU gene, bru1-3, has a phenotype causing reduced seed set, and the mutation is recessive (page 784, left column, paragraph 2-page 784, right column, paragraph 1).
Gherbi, Wright, and Takeda do not teach using RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence.
Dubois teaches a method using RNA interference by placing an RNAi construct under control of the pAlcA promoter to conditionally knock out the DUT1 gene in Arabidopsis (page 3, left column, paragraph 1). Dubois teaches a motivation to use a conditional RNA interference system because inactivation of the AtDUT1 gene is lethal (page 3, left column, paragraph 1). Dubois teaches that RNAi/DUT1 transformed plants have reduced expression of the target gene (page 3, left column, paragraph 2- right column paragraph 1, figure 3 A). Dubois teaches that RNAi/DUT1 plants had more than two recombination events per seedling, whereas control plants had no observed recombinant events, demonstrating that homologous recombination was increased in RNAi/DUT1 plants (page 5 right column paragraph 2-page 6, left column, paragraph).
Before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the method taught by Gherbi, Wright, and Takeda with the method of Dubois to further use RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence. One would have been motivated to do so in order to achieve a homozygous TONSOKU mutant phenotype with enhanced homologous recombination in a heterozygous mutant, or wildtype, line. Because the TONSOKU mutation is recessive, a heterozygous line would not have suffered from very low seed set (Takeda, page 784, left column, paragraph 2). Higher yield in stock lines are an obvious improvement to one of ordinary skill in the art. One would have had reasonable expectation of success because both Dubois and Gherbi, Wright, and Takeda taught methods to disrupt genes and proteins involved in the DNA repair and homologous recombination process in plants, and the methods of RNA interference were well understood at the time of filing. Thus, the method of reducing the level of TONSOKU polypeptide in a plant cell further comprising using RNA interference to reduce the expression of at least on TONSOKU nucleic acid sequence would have been obvious at the time of filing in view of Gherbi, Wright, Takeda, and Dubois.
Claims 1, 4-16, 21, 22, 24-27, 33, 36, & 38-42 are obvious in view of Gherbi, Wright, Takeda, and Dubois.
Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, as applied to claims 1, 4-15, 21, 22, 24-27, 33, 36, & 38-42 above, and further in view of Groth et al WO 2017/054832 A1 (published 4/6/2017, filed 9/30/2016), hereafter Groth.
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 4/6/2026, as applied to claims 1, 4-15, 18, 21, 22, 24-27, 33, 34, & 36-42. Applicant' s arguments filed 7/14/2026 have been fully considered (see response to Applicant’s Remarks above), but they are not persuasive.
Claim 18 is drawn to a method of reducing levels of a TONSOKU polypeptide in a plant cell comprising using an inhibitor to reduce or abolish an activity of the TONSOKU polypeptide.
The teachings of Gherbi, Wright, and Takeda are presented above. Gherbi, Wright, and Takeda do not teach using an inhibitor to abolish an activity of the TONSOKU polypeptide.
Groth teaches that an activity of the TONSL protein in human cells is to bind to post-replicative chromatin (page 52, lines 16-26 and figure 20) and that recognition of histone modification H4K20me0 is critical to this function (page 52 line 35-page 53, line4). TONSL is a homolog of TONSOKU protein found in animals (instant specification, page 9, paragraph 4). Groth teaches that mutated proteins are impaired in this function (page 52, lines 35-36 and figure 25 and 26). Groth also teaches a method of using an inhibitor to competitively bind TONSL to prevent normal chromatin binding activity (page 61, lines 9-14). Groth teaches that TONSL is involved in the repair of double strand breaks and damaged replication forks through homologous recombination (page 4, lines 22-25).
Before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the methods taught by Gherbi, Wright, and Takeda to reduce levels of a TONSOKU polypeptide in a plant cell with the method taught by Groth to reduce activity of a TONSOKU polypeptide in a plant cell by applying an inhibitor. Wright taught a motivation to increase homologous recombination (page 693, left column, paragraph 1) as well as a motivation to minimize untargeted genome mutations to improve public acceptance (page 703, left column, paragraph 3). Thus, one having ordinary skill in the art at the time of filing of the instant application could have been motivated to substitute the method comprising random mutation of Gherbi, Wright, and Takeda with the method of Groth to inhibit TONSOKU-homolog function using an inhibitor in order to improve public acceptance of the resulting plant. One would have had reasonable expectation of success because TONSOKU and TONSL are homologs and both were known in the art to play similar roles in the regulation of homologous recombination, and TONSL mutants phenocopy the effects of TONSL inhibitors (Groth, page 5, lines 17-19).
Thus, claims 1, 4-15, 18, 21, 22, 24-27, 33, 36, & 38-42 are obvious in view of Gherbi, Wright, and Takeda, in further view of Groth.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Victoria L DeLeo whose telephone number is (703)756-5998. The examiner can normally be reached M-F 8:00am-4pm EDT.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/VICTORIA L DELEO/Examiner, Art Unit 1662
/Anne Kubelik/Primary Examiner, Art Unit 1663
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