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
Applicant’s amendment of claims 1, 5, and 9 submitted on 01/23/2026 has been acknowledged. Applicant has added claim 11 as New claim. Since the new claim does not add search burden to applicant. the claim 11 is examined in this office action.
Thus claims 1, 5-9 and 11 are pending and are examined in this office action.
Rejections that are withdrawn
Objection to specification is withdrawn in light of applicant’s amendment of specification to include a proper symbols indicating use in commerce.
Argument to priority objection (Response to Rejection, page 11, paragraphs 1-5) was found persuasive therefore the priority objection was withdrawn and priority claim is acknowledged.
Objection to claim 4 is withdrawn in light of applicant’s cancellation of the claim.
35 USC § 102 rejection over claim 1 has been withdrawn in light of applicant’s amendment of claim 1 the modification are in uppercase letter of SEQ ID NO:3 and genetically modified potato kept in a dark place after an end of a post-harvest dormant period is 50% or less relative to a bud length of a genetically unmodified potato. The cited prior art Aharoni et al. does not disclose the limitation of the genetic modification in CSLM gene by introducing mutation in uppercase letter of SEQ ID NO:3 and the resulting modification cause 50% or less relative bud length compared to unmodified potato.
Nucleotide and/or Amino Acid Sequence Disclosures
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR § 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR §§ 1.821 through 1.825 for the reason(s).
These requirements will not be held in abeyance and must be addressed in response to this Office action.
Figures 4 and 5 fail to comply with the sequence rules.
Drawing Figures 4 and 5 has nucleic acid sequences that have more than 10 nucleic acid residues and applicant has added sequence identifiers (SEQ ID NO: ) however sequence listing showed there are only 23 sequences (see current listings) wherein applicant amended Figures 4 and 5 that states SEQ ID NOs: 24-30. Therefore the SEQ ID NOs: 24-30 are missing from sequence listings.
Each sequence with the specific mutation must have an independent sequence ID NO and must be listed in the sequence listing as an independent sequence.
Applicant must include each of the sequences and variants of sequences described in the specification or drawings as the disclosure of invention in the listings of the sequences.
Applicant are advised that the issue will not be held in abeyance.
If a sequence is presented in a drawing, the sequence must be included in the sequence listing if the sequence falls within the definition set forth in 37 CFR 1.821(a), see MPEP 2422.02.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not in sequence listings.
Required response – Applicant must provide:
New listings of the variants of sequences not currently in sequence listings.
Claim Interpretation
Claims 1, 5-9 and 11. recite a phrase “a genetically modified potato” that comprise genetic modification or a CSLM gene into which deletion, insertion, or substitution is introduced, is interpreted as the CSLM gene would be either endogenous or exogenous CSLM genes to the potato plant.
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 1, 5-9 and 11 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite in that it fails to point out what is included or excluded by the claim language. This claim is an omnibus type claim. All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim.
Claims 1, 5, 9 recite the phrase “uppercase region” which fails to point out what is included or excluded by the claim language. For example page 16, paragraph 0039, page 34, paragraph 0085 states “(TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA) SEQ ID NO:3”as example of partial sequence of CSLM gene identified by the protein binding to the CSLM. Furthermore such upper case letters are not present in sequence listing. Therefore it is not clear whether claim limits the uppercase letter as showed in specifications or it could be any other partial sequence of CSLM gene identified by any of the protein binding to the CSLM. For example Hassan et al. (Published: 2024, Journal: Plant And Cell Physiology,66(1), 101–119 doi:https://doi.org/10.1093/pcp/pcae145) teaches the catalytic activity of at least one member of most of the Csl families has been reported (CslA–H, J, and M). Hassan et al. teaches some CSLM has non-cell wall function, some has function in saponin biosynthesis, has function as C3 glucuronosylation of triterpenoid aglycones in some but not but not all CslMs and in soybean only three of five CslMs were coexpressed with other triterpenoid pathway genes having glucuronosyl transferase activity (page 102, left paragraph 3), therefore there would have been diverse proteins binding to the different regions of the CSLM gene as SEQ ID NO:2.
For following analysis it is based on the assumption that the upper case letter of SEQ ID NO:3 are as showed as in (TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA) (Spec, page 16, paragraph 0039)
Claim Rejections - 35 USC § 112 – written description requirements
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.
Claims 1, 5-9 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.
Analysis of Breadth of Claims
Claims recite large variants of nucleotide sequences having 80% sequence identity to SEQ ID NO:2 and their variants of protein sequences.
Claim recite any deletions, insertions or substitution in any of any CSLM gene in the sequence having at least 90% identity to uppercase letter of SEQ ID NO: 3 would lead to potato having 80% sequence identity to SEQ ID NO:2 would cause less than 20% or less solanine content and chaconine content (claims 1, 5 and 6) or bud length 50% or less (claim 4).
The compared genetically unmodified potato plant would have any variations in chalconine, solanine contents or bud length across potato germplasms (claims 1, 5, and 9).
What is Described in the Specification
Applicant describes:
cellulose synthase-like M gene (CSLM 9ene) Sotub07g016530.1.1, which is, co-expressed with a glycoalkaloid biosynthesis gene next to chromosome 12 of the glycoalkaloid biosynthesis gene in the genome database (Spud DB: http:// solanaceae. plant biology. msu. edu/ index. shtml) of the potato (S. tuberosum) (page33, lines 2-7).
CSLM gene include a base sequence encoding a protein having an amino acid sequence of SEQ ID NO: 1 or SEQ ID No:22 (page 7, lines 13-17) which are encoded by SEQ ID NO:2 or SEQ ID NO:23 (page 8, lines 5-8).
Based on the genomic DNA sequence of potato variety “Sassy” (page 34, paragraph 0083), platinum TALEN vector pSuehiro117 identifying the uppercase regions of the sequence of SEQ ID NO:3 (TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA) was prepared (page 34, lines 26-27 and page 35, lines 1-3).
pSuehiro117 #343 (Figure 4) and pSuehiro117 #389 (Figure 5) were the genome-edited plants (page 37, paragraph 0091).
No generation of glycoalkaloid in pSuehiro117 #343 and pSuehiro117 #389 as depicted in Fig. 6 (page 39, line 12).
the edited plant had smaller bud length and increased hardness (i.e. inhibited aging) compared to non-transferred Sassy (page 41, Table 1).
Difference Between What was Described and What is Claimed
Applicant has not described any deletions, insertions or substitution in any of CSLM gene leading to potato having 80% sequence identity to SEQ ID NO:2 would cause less than 20% or less solanine content and chaconine content or bud length 50% or less (claims 1, 5 and 6).
Applicant has not described any of the plant that would have less than 20% or less solanine content and chaconine content compared to any of genetically unmodified plant other than the control potato plant not comprising the modified CSLM gene since there are variations in chalconine and solanine contents across potato germplasms (claims 1, 5, and 9).
Applicant has not described any guide RNA targeting a CSLM gene comprising a region having 90% sequence identity to the uppercase letter of SEQ ID NO:3 other than with the target as SEQ ID NO: 3 would cause potato with solanine and chaconine content to be 20% or less and 50% or less relative to a bud length.
Applicant has not described any modified plant other than pSuehiro117 #343 and pSuehiro117 #389 that would have solanine and chaconine content to be 20% or less and bud length 50% or less compared to the control unmodified plant.
Applicant has not described the uppercase region of the SEQ ID NO:3 other than as showed in “TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA” (page 16, paragraph 0039, lines 21-23).
Analysis
The purpose of the written description is to ensure that the inventor had possession at the time the invention was made, of the specific subject claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
Applicant has not described any deletions, insertions or substitution in any of CSLM gene leading to potato having 80% sequence identity to SEQ ID NO:2 would cause less than 20% or less solanine content and chaconine content or bud length 50% or less (claims 1, 5 and 6). The recited potato plant would comprise any number of the additions, deletions or substitution anywhere in the CSLM gene leading to 80% sequence identity to SEQ ID NO:2. SEQ ID NO:2 is 1443 nucleotide long and it encodes SEQ ID NO:1 that which is 480 amino acid long (page 8, lines 5-8). For example a variant of SEQ ID NO:2 having at least 90% identity would have 144 NA changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 2, and this encompasses a genus of nucleic acid sequence that includes at least ~4144 different molecules. For this reason, the genus of nucleic acid molecules having at least 90% identity to SEQ ID NO: 2 is a very large genus of molecules. Similarly the mutation causes large variants of protein sequences that would require to have the characteristics of less than 20% or less solanine content and chaconine content or bud length 50% or less.
Furthermore, the state of the art at the time of the instant invention was that although the skilled artisan would appreciate the specific deletion in the uppercase letter of SEQ ID NO: 3, one would not be able to readily predict function of inserting in a nucleic acid sequence which has at least 90% identity to uppercase letter of SEQ ID NOs: 3 that would encode function of polypeptide encoded by a nucleotide having at least 80% identity to SEQ ID NO: 2 and it is impossible to predict such a broad sequence variation will have any required function. For example, Guo et al. (Published Year: 2004, Journal: Proceedings of the National Academy of Sciences, Vol. 101(25), pages: 9205-9210) teaches that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (page 9209, right. col., paragraph 2).
Instead applicant has not described modified CSLM gene in a potato plant comprising any variant of SEQ ID NOs: 2 having at least 80% identity with the recited properties of for example less than 20% or less solanine content and chaconine content or bud length 50% or less.
The recitation of any numbers of additions, deletions or substitution would create a modified potato plant with any genomic structure that only required to have at least 80% identity to SEQ ID NO:2. Instead applicant has not described any plant other than the modification caused by a TALLEN targeting SEQ ID NO:3 (having parts of SEQ ID NO:2) that would produce gene edited plant pSuehiro117 #343 and pSuehiro117 #389 that would have 20% or less solanine content and chaconine content or bud length 50% or less (claim 4).Then there is dearth of description of any deletions, insertions or substitution in any of CSLM gene in a potato cause less than 20% or less solanine content and chaconine content or bud length 50% or less (claim 4).
For example, Jozwiak et al. (Published: 2024, Journal: Science 386, 1365 adq5721, pages 1-14) teaches Genes associated with steroidal glycoalkaloids SGA biosynthesis (i.e. production of solanine and chaconine) in potato are coexpressed and some of them localized to the same genomic region forming a metabolic gene cluster (see Figure 1A) wherein the cluster include StSGT3, St16DOX, StPGA2 and StSGT1 from potato and GAME1, GAME2, GAME6, GAME11, GAME15, GAME17, and GAME18 in tomato wherein GAME 15 is annotated as cellulose synthase M genes (page 1, right paragraph 2). Thus there are many genes with various nucleotide structures present in potato that would affect SGC biosynthesis.
Furthermore, Hassan et al. (Published: 2024, Journal: Plant And Cell Physiology,66(1), 101–119 doi:https://doi.org/10.1093/pcp/pcae145) teaches the catalytic activity of at least one member of most of the Csl families has been reported (CslA–H, J, and M). Hassan et al. teaches some CSLM has non-cell wall function, some has function in saponin biosynthesis, has function as C3 glucuronosylation of triterpenoid aglycones in some but not but not all CslMs and in soybean only three of five CslMs were coexpressed with other triterpenoid pathway genes having glucuronosyl transferase activity (page 102, left paragraph 3). Furthermore, Hassan et al. teaches SOAP5-related CslM genes and separated class into two CsLM clades as CslM1 (for the clade with a presumed ‘cell wall function’) and CslM2 [CSyGT , the phylogenetically distinct clade with glycosylation activity on specialized metabolites]. Therefore, there will be various structure and function of the CSLM genes. Little et al. (Published; 2018, Journal: Plant Physiology, 177: pp. 1124–1141) teaches CslM lineage of gene family is shown to be widely distributed in eudicots (page 1125, right last paragraph, see figure 1 below). Little et al. teaches eudicot-specific CslM genes underwent multiple duplication events early in the history of this group and subsequently within several sampled species, and they experienced frequent gene losses in each major subclade (Fig. 3) (page 1129, left last paragraph). Furthermore, Chung et al. (Published: 2020, Journal: Nature Communications 11:5664 | https://doi.org/10.1038/s41467-020-19399-0) teaches CslMs were widely distributed among eudicots, and multiple genes were found in most plant species (page 4, last paragraph, see page 6, Figure 5).
Instead applicant has described genome sequence of CSLM gene was of potato variety “Sassy” which was carried out based on sequence of the Sotub07g016530.1.1 (i.e. SEQ ID NO: 2) that encodes SEQ ID NO:1 (page33, lines 9-13; and page 34 and lines 5-15) wherein the PCR was carried out and was cloned into vector to the gene segments, and absence of SEQ ID NO:3 which identified by TALLEN vector. Therefore, applicant has modified SEQ ID NO: 2 in the variety “Sassy”.
Therefore, there will be various structure and function of the genetically modified CSLM gene as SEQ ID NO:2. Thus there is dearth of description of insertion, deletion and substitution in SEQ ID NO:2 leading to a sequence having 80% sequence identity to SEQ ID NO:2 would cause less than 20% or less solanine content and chaconine content or bud length 50% or less (claim 4) other than the gene encoding the protein of SEQ ID NO:1.
Applicant has not described any of the plant that would have less than 20% or less solanine content and chaconine content or bud length 50% or less compared to any of genetically unmodified plant since there are variations in chalconine and solanine contents in unmodified potato germplasms. For example, Zhou et al. (Published: 2025, Journal: BMC Plant Biology 25:725 https://doi.org/10.1186/s12870-025-06766-6) teaches in a sample of 117 potato tubers α-solanine content in the tuber cortex ranged from 18.95 to 1123.49 mg/kg DW with coefficients of variation ranging from 90.79% to 92.68% and the α-chaconine content ranged from 34.22 to 974.28 mg/kg DW with coefficients of variation ranging from 57.94% to 66.79% (page 4, left last and right first paragraph). Furthermore, Baguchi et al. (Published: Journal:1980, American potato journal, 57:151-157) teaches budding length of ten cultivars varied from 5 to 22 mm per tuber at the end of dormancy and from 16 to 122mm after 14 days of sprouting (page 155, paragraph 3 and Figure 3).
Therefore, there would be large variations in the unmodified potato to compare to any of the modification of potato comprising any of a deletion, insertion or substitution in CSLM gene. Therefore, there is dearth of description of comparison of modified potato to any unmodified potato with less than 20% or less solanine content and chaconine content or bud length 50% or less.
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Applicant has not described any guide RNA targeting a CSLM gene other than with the target as in SEQ ID NO: 3 (claims 7 and 9) would cause potato with solanine and chaconine content to be 20% or less (claims 7 and 9). Applicant describes based on the genomic DNA sequence of potato variety “Sassy” (page 34, paragraph 0083), platinum TALEN vector pSuehiro117 identifying the uppercase regions of the sequence of SEQ ID NO:3 (TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA) was prepared and used for gene editing (page 34, lines 26-27 and page 35, lines 1-3). The SEQ ID NO:3 comprises about 34 nucleotides of uppercase region wherein a sequence having 90% sequence identity to uppercase region of SEQ ID NO:3 would include variants of the upper case region with at least 3 nucleotide addition, substitution and deletions and that would comprise genus of nucleic acids comprising 43 molecules with different target regions.
Furthermore, Figure 4 and 5 teaches the sequence with low solanine and chaconine content had many of the sequence for example first 7 sequences and all the sequence except the last two sequence in pSuehiro117 #343 and pSuehiro117 #389 respectively comprise deletion in lowercase letter (i.e. not in the uppercase lettered sequence having at least 90% identity to SEQ ID NO:3) wherein Figure 6 showed the mutant sequence had effect as decreased solanine and chaconine content. Thus applicant has not described which of the sequence deletion either uppercase, lowercase or both caused the decrease in solanine and chaconine content and it is not clear strictly deleting, inserting or substitution in the upper case letter of SEQ ID NO:3 would cause decrease in salonine and chaconine content.
Jozwiak et al. teaches when they use CRISPR Cas9 editing using four sets of SNPs, the insertion deletion were only found by sgRNA2 leading to knockout and reduction in SGA content of solanine and chaconine accumulation (see figure S21 and snippet of Figure 6 below).. Therefore, there is dearth of description of any plant with any guide RNA targeting any site of the CSLM gene would cause reduction in solanine and chaconine accumulation. Therefore, there is dearth of description of any guide RNA targeting a CSLM gene other than with the target as specific region of SEQ ID NO: 3 (claims 7 and 9) would cause potato with solanine and chaconine content to be 20% or less (claims 7 and 9). Furthermore, alignment of Applicant’s SEQ ID NO:22 as CSLM has 100% sequence identity to the potato GAME 15 of Jozwiak et al. (see enclosed PDF).
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Accordingly, the claims are drawn to an extremely large genus of any of CSLM gene variants, large variants of targets of any CSLM gene variants and any unmodified plant encompassing any possible yet unspecified mutated genes associated with the claimed phenotype of less than 20% or less solanine content and chaconine content and less than 50% or less relative to a bud length, when Applicants have only describes specific deletions on gene encoding SEQ ID NO: 1. The claims are drawn to any unspecified CSLM gene and modified potato plant comprising any numbers of deletions, insertion and substitutions vs. the exemplified specific deletion carryout out using TALLEN vector identifying regions of SEQ ID NO:3 for gene encoding SEQ ID NO: 1 in the Specification.
Applicant has not described the uppercase region of the SEQ ID NO:3 other than as showed in “TGCAAAGATTCCGATCTaccaccaattgacgtAATGGTATTCACTGCCA” (page 16, paragraph 0039, lines 21-23). The recited uppercase region of the SEQ ID NO:3 has been shown in specification, page 16, paragraph 0039, lines 21-23). The sequence listing does not show any upper case letters.
Relating to structure vs. function, the claims remain drawn to any unspecified potato plant comprising mutated CSLM gene variants having a nucleotide sequence having 80% identity to SEQ ID NO:2 and carried out by any guide RNA. This leads to a situation where the instantly claimed gene variants of CSLM would not possess the necessary structural features needed to accomplish the claimed phenotype. The Specification makes clear that the specific deletion carryout out using TALLEN vector identifying regions of SEQ ID NO:3 for gene encoding SEQ ID NO: 1 lead to the specific recited phenotypes, thus it is necessary to claim the plant, composition and method as such (i.e., specific target regions, sequences and plant).
The test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to one skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad Pharm, Inc, v EH Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Lockwood v. Amer. Airlines, ina, 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). "An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations. Lockwood, 107 F.3d at 1572, 41 USPG2d at 1966". While the written description requirement does not demand either examples or an actual reduction, actual "possession" or reduction to practice outside of the specification is not enough. Ariad Pharm, Inc. v. Eli Lilly & Co., 598 F,3d 1336,1352 (Fed. Cir. 2010). Rather, it is the specification itself that must demonstrate possession. Id.
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. As a result, it is not clear that Applicant was has described the structure of claimed genus to have application as recited function at the time this application was filed.
Following analysis of rejection under 35 USC § 103 has been modified and previous 102 rejection for claim 1 has been analyzed under 35 USC § 103 since applicant has added the limitation of the modification are in uppercase letter of SEQ ID NO:3 and genetically modified potato kept in a dark place after an end of a post-harvest dormant period is 50% or less relative to a bud length of a genetically unmodified potato.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Obvious over Aharoni et al. and further in view of Liu et al. , Hartmann et al., and Nakayasu et al.
Claims 1, 5-9 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Aharoni et al. (US patent Pub. No.: US 2019/0059314 A1, Pub. Date: Feb. 28, 2019), and further in view of Liu et al. (Published: 2012, Journal: Mol Biol Rep 39:11277–11287) and, further in view of Hartmann et al. (Published: 2011, Journal: Plant Physiology 155: 776–796), and further in view of Nakayasu et al. (Published: 2018, Journal: Plant Physiology and Biochemistry 131: 70–77), and as evidenced by Jowiak et al.
Claims are drawn to a genetically modified potato and a method of producing the same, comprising a CSLM gene into which deletion, insertion, or substitution is introduced at uppercase letter of sequence having at least 90% identity to SEQ ID NO:3, wherein the sequence has at least 80% sequence identity to SEQ ID NO:2, and wherein a solanine content, or a chaconine content is 20% or less and bud length is 50% or less compared to an unmodified plant. The claims are further drawn to the method is carried out by genome editing agent.
Regarding claim 1, since any deletion, insertion, or substitution introduced into a uppercase region of SEQ ID NO:3, the potato would have any genomic structure, the plant has been only described by its function of the chaconine content of the genetically modified potato is 20% or less, relative to a solanine content, or a chaconine content, or both the solanine content and the chaconine content of a genetically unmodified potato, respectively. Therefore, any plant having such functions would anticipate the claim.
The claim is interpreted as “product by process claim” wherein [E]ven though product by process claims are limited by and defined by the process, determination of patentability is based on the product itself. If the product in the product by process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process."
Aharoni et al. discloses in leaves of genetically modified transgenic potato lines with RNA interference as GAME15-RNAi lines #1, #2 and #3 the levels of a-solanine and a-chaconine in leaves were 20% or less (page 5, paragraph 0052, see Figure 16 below). Aharoni et al. discloses GAME15i was silenced in potato (#1, #2, and #3) to determine its effect on potato SGAs metabolism (page 35, paragraph 0253).
Aharoni et al. discloses Aharoni et al.’s GAME 15 is a cellulose synthase-like protein (page 3, paragraph 0030).
Furthermore, alignment of Applicant’s SEQ ID NO: 22 to the SEQ ID NO: 37 of the Aharoni et al. shows the sequence has 100% sequence identity with first 4 amino acid sequence missing. Therefore, the modified potato plant of Aharoni et al. with first 4 deletion would be the genomic structure claimed by applicant in claim 1 for the claimed modified potato plant.
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Query: unnamed protein product Query ID: lcl|Query_5059353 Length: 711
>unnamed protein product
Sequence ID: Query_5059355 Length: 715
Range 1: 5 to 715
Score:1473 bits(3813), Expect:0.0,
Method:Compositional matrix adjust.,
Identities:711/711(100%), Positives:711/711(100%), Gaps:0/711(0%)
Query 1 MELNKSTVPQPITTIYRLHMFIHSIIMVALIYYRVSNLFKFENILSLQALAWVLITFGEF 60
MELNKSTVPQPITTIYRLHMFIHSIIMVALIYYRVSNLFKFENILSLQALAWVLITFGEF
Sbjct 5 MELNKSTVPQPITTIYRLHMFIHSIIMVALIYYRVSNLFKFENILSLQALAWVLITFGEF 64
Query 61 SFILKWFFGQGTRYRPVERDVFPENITCKDSDLPPIDVMVFTANPKKEPIVDVMNTVISA 120
SFILKWFFGQGTRYRPVERDVFPENITCKDSDLPPIDVMVFTANPKKEPIVDVMNTVISA
Sbjct 65 SFILKWFFGQGTRYRPVERDVFPENITCKDSDLPPIDVMVFTANPKKEPIVDVMNTVISA 124
Query 121 MALDYPTDKLAVYLADDGGCPLSLYAMEEACVFAKLWLPFCRKYGIKTRCPKAFFSPLGD 180
MALDYPTDKLAVYLADDGGCPLSLYAMEEACVFAKLWLPFCRKYGIKTRCPKAFFSPLGD
Sbjct 125 MALDYPTDKLAVYLADDGGCPLSLYAMEEACVFAKLWLPFCRKYGIKTRCPKAFFSPLGD 184
Query 181 DERVLKNDDFDAEMKEIKLKYEEFQQNVERAGESGKINGNVVPDRASFIKVINDRKAESE 240
DERVLKNDDFDAEMKEIKLKYEEFQQNVERAGESGKINGNVVPDRASFIKVINDRKAESE
Sbjct 185 DERVLKNDDFDAEMKEIKLKYEEFQQNVERAGESGKINGNVVPDRASFIKVINDRKAESE 244
Query 241 KSADDLTKMPLLVYVSRERRFNRLHHFKGGSANALLRVSGIMSNAPYILVLDCDFFCHDP 300
KSADDLTKMPLLVYVSRERRFNRLHHFKGGSANALLRVSGIMSNAPYILVLDCDFFCHDP
Sbjct 245 KSADDLTKMPLLVYVSRERRFNRLHHFKGGSANALLRVSGIMSNAPYILVLDCDFFCHDP 304
Query 301 ISARKAMCFHLDPKLSSDLAYVQFPQVFYNVSKSDIYDVKIRQAYKTIWHGMDGIQGPVL 360
ISARKAMCFHLDPKLSSDLAYVQFPQVFYNVSKSDIYDVKIRQAYKTIWHGMDGIQGPVL
Sbjct 305 ISARKAMCFHLDPKLSSDLAYVQFPQVFYNVSKSDIYDVKIRQAYKTIWHGMDGIQGPVL 364
Query 361 SGTGYFLKRKALYTSPGVKEEYLSSPEKHFGRSKKFLASLEEKNGYVKAEKVISEDIVEE 420
SGTGYFLKRKALYTSPGVKEEYLSSPEKHFGRSKKFLASLEEKNGYVKAEKVISEDIVEE
Sbjct 365 SGTGYFLKRKALYTSPGVKEEYLSSPEKHFGRSKKFLASLEEKNGYVKAEKVISEDIVEE 424
Query 421 AKTLATCAYEDGTHWGQEIGYSYDCHLESTFTGYLLHCKGWRSTYLYPDRPSFLGCAPVD 480
AKTLATCAYEDGTHWGQEIGYSYDCHLESTFTGYLLHCKGWRSTYLYPDRPSFLGCAPVD
Sbjct 425 AKTLATCAYEDGTHWGQEIGYSYDCHLESTFTGYLLHCKGWRSTYLYPDRPSFLGCAPVD 484
Query 481 MQGFSSQLIKWVAALTQAGLSHLNPITYGFSSRMKTLQCMCYAYLIYFTLYSWGMVLYAS 540
MQGFSSQLIKWVAALTQAGLSHLNPITYGFSSRMKTLQCMCYAYLIYFTLYSWGMVLYAS
Sbjct 485 MQGFSSQLIKWVAALTQAGLSHLNPITYGFSSRMKTLQCMCYAYLIYFTLYSWGMVLYAS 544
Query 541 VPSIGLLFGFQVYPDVHDPWFAVYVIAFISAILENMSESIPDGGSFKSWWMEYRALMMMG 600
VPSIGLLFGFQVYPDVHDPWFAVYVIAFISAILENMSESIPDGGSFKSWWMEYRALMMMG
Sbjct 545 VPSIGLLFGFQVYPDVHDPWFAVYVIAFISAILENMSESIPDGGSFKSWWMEYRALMMMG 604
Query 601 VSAIWLGGLKAILDRIIGTEGEKLYLSDKAIDKEKLKKYEKGKFDFQGIGILAVPLIAFS 660
VSAIWLGGLKAILDRIIGTEGEKLYLSDKAIDKEKLKKYEKGKFDFQGIGILAVPLIAFS
Sbjct 605 VSAIWLGGLKAILDRIIGTEGEKLYLSDKAIDKEKLKKYEKGKFDFQGIGILAVPLIAFS 664
Query 661 LLNLVGFIVGANHVFITMNYAGVLGQLLVSSFFVFVVVTVVIDVVSFLKVS 711
LLNLVGFIVGANHVFITMNYAGVLGQLLVSSFFVFVVVTVVIDVVSFLKVS
Sbjct 665 LLNLVGFIVGANHVFITMNYAGVLGQLLVSSFFVFVVVTVVIDVVSFLKVS 715
Jowiak et al. shows the evidence that cellulose synthase–like M gene in potato (i.e. CSLM as stGAME15) (page 1, right paragraphs 2-3, see snippet of figure 1 below). Jowiak et al. teaches potato GAME15 RNA interference (GAME15i) lines (fig. S10) showed notable reduction in SGA content of solanine and chaconine accumulation and high accumulation of cholesterol (page 4 and 5, last and first paragraph respectively).
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Jozwiak et al. utilizes potato cultivar “Sassy” and Desiree for RNAi and to create CRISPR-Cas9 mutant plants in potato (page 10, left paragraphs 5-6).
The European cultivated potato database accessed at https://www.europotato.org/varieties/view/Sassy-P#:~:text=Varieties,Breeder%20Agent%20Germicopa%20UK, accessed in 10/23/2025 showed the evidence that the cultivar “Sassy” was developed before 2004. Government of Canada website accessed at https://inspection.canada.ca/en/plant-health/potatoes/potato-varieties/desiree, accessed in 10/23/2025, showed the evidence that the potato cultivar “Desiree” was registered in Canada in 1994 and bred from the cross (Urgenta x Depesche) made by ZPC in Leeuwarden, The Netherlands, in 1951. Therefore, the lines existed before effective filing date of invention.
Furthermore, alignment of Applicant’s SEQ ID NO:22 as CSLM has 100% sequence identity to the potato GAME 15 (i.e. a cellulose synthase–like M gene (CSLM) in potato) of Jozwiak et al. (see enclosed PDF and table S1 of Jozwiak et al.).
Therefore Aharoni et al.’s modified potato line Desiree (page 19, paragraph 0213) would have the same genomic structure as the applicant’s plant claimed in claim 1 and the modified gene would be synthase–like M gene in potato (i.e. CSLM) as evidenced by Jozwiak et al.
Aharoni et al. does not teach their mutant potato has 50% or less relative bud length compared to any of a unmodified potato.
Liu et al. teaches difference in bud length in the potato tubers are controlled by the genetics of the plants (page 11278, right paragraph 2, page 11277, Abstract). Liu et al. teaches their disclosed genes would have potential targets for the genetic engineering of potato dormancy and sprouting to suppress sprouting during storage and transport (page 11286, left first paragraph). Liu et al. teaches accelerated or delayed sprouting of the harvested tubers may be favored depending on the intended purpose (page 11278, left paragraph 2) wherein prolonging dormancy would be useful when tubers serve as food and raw materials of industrial processing (page 11278, right paragraph 1).
Furthermore, Hartmann et al. teaches genes involved in the biosynthesis of cellulose (cellulose synthase), gene involved in cell wall biosynthesis, assembly and modification, were found to be induced exclusively in wild-type tubers (Supplemental Tables S1 and S2) (page 786, left paragraph 1). Therefore, someone skilled in the art would screen for changing in bud length and sprouting in the mutant tuber plant for cellular synthase gene such as CSLM gene.
Aharoni et al., Liu et al. and Hartmann et al. does not teach the deletion, insertion and substitution was carried out by enzyme including a nuclease or a deaminase domain. Nakayasu et al. teaches method of creating deletion, addition and substitution using CRISPR/Cas9 system comprising Cas9 nuclease and multiplex gRNA (page 71, right paragraph 2).
Nakayasu et al. teaches CRISPR/Cas9 mediated targeted deletion of St16DOXgene and deletion mutants produced by the deletion of the gene (page 73, right last two paragraphs) and some deleted lines showed no detectable levels of solanine and Chaconine (Figure 2, see figure below).
Therefore it would have been obvious to a skilled in the art before the effective date of filling of the invention from some teaching, suggestions and motivation to modify the CSLM as GAME15 as taught by Aharoni et al. that would leads to the potato plant with solanine content, or a chaconine content is 20% or less. Someone skilled in the art would screen for the shorter bud length in segregating population comprising modified gene of the Aharoni et al. which would have been more efficiently modified using the enzyme including nuclease domain as Cas9 to obtain plant with shorter bud length leading to the bud length to be 50% or less relative to any bud length of a genetically unmodified potato as suggested by Liu et al. and Hartman et al. that cellulose synthase is involved in cell wall biosynthesis and modifications. The deletion, insertions and substitution in uppercase letter of SEQ ID NO:3, would produce any of the variants of the SEQ ID NO:2 with 80% identity.
Regarding claims 5-7, Aharoni et al. claims 20-26 teach a method of reducing the content of at least one steroidal alkaloid (solanine, chaconine and their derivatives), in a modified potato plant, the method comprising: (b) mutagenizing a cellulose synthase-like proteins which is GAME15, wherein the mutagenesis comprises introduction of one or more point mutations into the gene, or genome editing, or use of a bacterial CRISPR/CAS system, or a combination thereof. Aharoni et al. teaches CRISPR/Cas system comprises Cas nuclease (i.e. enzyme of nucleic acid metabolism) and a guide RNA molecule that bind to the endogenous target site (page 15, paragraph 0167).
Aharoni et al. teaches in leaves of genetically modified transgenic potato lines with RNA interference as GAME15-RNAi lines #1, #2 and #3 the levels of a-solanine and a-chaconine in leaves were 20% or less (page 5, paragraph 0052, see Figure 16 below). Aharoni et al. teaches GAME15i was silenced in potato (#1, #2, and #3) to determine its effect on potato SGAs metabolism (page 35, paragraph 0253).
Aharoni et al. claim 21 teaches Aharoni et al. GAME 15 is a cellulose synthase-like protein.
Aharoni et al. does not show example where their genetically modified plant comprise deletion, insertions or substitutions.
Nakayasu et al. teaches method of creating deletion, addition and substitution using CRISPR/Cas9 system comprising Cas9 nuclease and multiplex gRNA (page 71, right paragraph 2). Nakayasu et al. teaches CRISPR/Cas9 mediated targeted deletion of St16DOXgene and deletion mutants produced by the deletion of the gene (page 73, right last two paragraphs) and some deleted lines showed no detectable levels of solanine and Chaconine (Figure 2, see figure below).
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Therefore, it would have been obvious before the effective date of filling of the invention from teaching, suggestions and motivation of Aharoni et al. to develop a method for producing genetically modified potato comprising introducing deletion, insertion of substitution into a CSLM gene of a potato to produce a potato plant comprising solanine and chaconine content to be 20% or less, relative to a genetically unmodified potato using RNAi and CRISRPR/Cas9 system. Furthermore, from teaching of Nakayasu et al. for targeted deletion of a gene in potato to reduce the solanine and Chaconine content using CRISRPR/Cas9 system. Someone skilled in the art would screen for the shorter bud length in segregating population comprising modified gene of the Aharoni et al. which would have been more efficiently modified using the enzyme including nuclease domain as Cas9 to obtain plant with shorter bud length leading to the bud length to be 50% or less relative to any bud length of a genetically unmodified potato as suggested by Liu et al. and Hartman et al. that cellulose synthase is involved in cell wall biosynthesis and modifications.
Regarding claim 8, Aharoni et al. teaches the Cas9 comprise nuclease domain (page 15, paragraph 0167).
Regarding claim 9, the composition comprising a Cas9, gRNA and the CSLM gene that would produce a potato plant comprising solanine and chaconine content to be 20% or less, relative to a genetically unmodified potato plant.
Regarding claim 11, since the modification is carried out by any deletion, insertion and substitution (i.e. would add, delete or substitute any base or combination of bases) as recited in claim 11, the modified SEQ ID NO:2 with 80% identity to SEQ ID NO:2 would have any structure and Aharoni et al.’s GAME 15 would have been one of the species of the modification recited in the claim.
Response to Arguments
Applicant's arguments filed 01/23/2026 have been fully considered but they are not persuasive.
Applicant argues RNAi does not introduce any deletion, insertion, or substitution into the endogenous genomic DNA sequence. Applicant argues in Aharoni's lines, the genomic DNA at the CSIM (GAME15) locus remains completely intact and wild-type (Response to Rejection, page 15, second paragraph). Applicant argues in contrast, claim 1 specifically requires a "genetically modified potato" comprising a CSIM gene into which "deletion, insertion, or substitution is introduced into: (i) an uppercase region of SEQ ID NO: 3." This is a physical, permanent alteration of the genomic DNA template itself (Response to Rejection, page 15, paragraph 3).
Applicant argues the Office interprets the claim as a product-by-process claim and asserts that the products are identical. Applicant argues however, for biological molecules and modified organisms, the structure of the genome itself is a defining physical characteristic of the product. Applicant argues a potato with a wild-type CSIM gene (but suppressed by RN Ai) and a potato with a truncated or disrupted CSIM gene (edited at SEQ ID NO: 3) are structurally distinct chemical entities. Applicant argues the edited genome of the present invention is not "the same as or obvious from" the wild-type genome of Aharoni's RNAi lines (Response to Rejection, page 15, second to last paragraph).
Applicant argues the physical modification of the genomic DNA at the site of SEQ ID NO: 3 provides a functional phenotype that Aharoni does not achieve. Applicant argues as demonstrated in the Specification, while mere silencing of SGA genes (like SSR2) fails to suppress budding, the site-specific genomic editing of CSLM at SEQ ID NO: 3 uniquely results in a 50% or more reduction in bud length and inhibited tuber aging (Response to Rejection, page 16, first paragraph).
Applicant argues since Aharoni et al. does not edit the genomic DNA at SEQ ID NO: 3, and does not disclose the resulting sprout-inhibition phenotype, Aharoni et al. fails to anticipate the claimed invention (Response to Rejection, page 16, paragraph 2).
Applicant argues While Jozwiak mentions CRISPR-Cas9 and the cultivar "Sassy," Applicant argues the reference does not provide a prior art potato line that contains the specific genomic modification in the CSIM gene as defined by SEQ ID NO: 3 therefore the Office Action cannot establish a prima facie case of anticipation vis-à-vis claim 1 (Response to Rejection, page 16, paragraph 3).
Applicant argues claims 5 and 9 have been amended so as to recite substantially the same features as claim 1. Applicant argues Nakayasu focuses on SSR2, and the present Specification proves that silencing SSR2 (or PGA4) cannot suppress budding (e.g., "[o]n the other hand, knockdown of SSR2 and PGA4, which are genes associated with synthesis of chaconine, cannot suppress budding of potatoes. Applicant argues the mechanism for controlling budding has not been understood." See Nakayasu). Applicant argues this demonstrates that the mechanism for controlling budding was not understood and could not be predicted simply by reducing SGA levels (Response to Rejection, pages 16and 17, last and first paragraphs).
Applicant argues a basis for how Aharoni is deficient vis-a-vis the noted feature of claim 1 has been discussed above and the OC does not rely upon Nakayasu to compensate for this deficiency, and nor does Nakayasu compensate for this deficiency and at least one element is not obvious from the combination of the references (Response to Rejection, page 17, paragraph 2-3).
Applicant assert Liu et al. identifies numerous genes expressed during dormancy release and Hartmann et al. discusses the role of phytohormones (cytokinin and gibberellin) in sprout growth. Applicant argues neither reference provides any suggestion that the CSLM (GAME15) gene-a cellulose synthase-like protein-functions as a key regulator of physical sprout elongation (Response to Rejection, page 17 second to last paragraph).
Applicant argues Liu et al. provides a broad list of ESTs associated with dormancy breaking but does not demonstrate that genomic modification of the CSLM gene results in a 50% or more reduction in bud length. Applicant argues Hartmann et al. focuses on hormone-mediated meristem reactivation. Applicant argues it does not teach that a gene involved in the secondary metabolism (SGA biosynthesis) like CSLM could also exert a profound mechanical or physiological inhibition on sprout growth (Response to Rejection, pages 17 and 18, last and first paragraphs).
Applicant argues core of the Office's rejection relies on the assumption that suppressing SGA levels (as taught by Aharoni) would naturally lead to sprout suppression (as discussed generally in Liu/Hartmann). Applicant argues the present specification provides experimental evidence that contradicts this assumption (Response to Rejection, pages 17 and 18, paragraph 2).
Applicant argue as shown in Comparative Example 1 (SSR2-edited lines), even when SGA content is drastically reduced, budding is not suppressed. Applicant argues this technical fact establishes that SGA reduction and sprout inhibition are dissociated physiological phenomena (Response to Rejection, page 18, paragraph 3).
Applicant argues because Liu and Hartmann only provide general teachings on tuber dormancy and do not link the specific CSLM/SGA pathway to sprout length, a person of ordinary skill in the art (PHOSIT A) would have had no "reasonable expectation of success" that targeting the CSLM gene specifically would achieve the claimed synergistic dual effect of SGA reduction and significant budding delay (Response to Rejection, page 18, paragraph 4).
Applicant argues the claimed invention inhibits the softening (aging) of tubers during storage. Applicant argues neither Liu et al. nor Hartmann et al. addresses the maintenance of tuber hardness through the specific genomic modification of the CSLM gene at the site of SEQ ID NO: 3.
Applicant's arguments have been fully considered but they are not persuasive since claim 1 is directed to a potato plant wherein in its genome it comprise a sequence having 80% identity to the SEQ ID NO:2.
Regarding argument for specific trait Aharoni et al. discloses in leaves of genetically modified transgenic potato lines with RNA interference as GAME15-RNAi lines #1, #2 and #3 the levels of a-solanine and a-chacocine in leaves were 20% or less (page 5, paragraph 0052, see Figure 16 below). Aharoni et al. discloses GAME15i was silenced in potato (#1, #2, and #3) to determine its effect on potato SGAs metabolism (page 35, paragraph 0253). Regarding argument on specific mutation is required to be in the uppercase region of SEQ ID NO:3, there is no limit of any of possible structures resulting to a nucleotide sequence by any of the deletion, insertion and substitutions in the uppercase region of SEQ ID NO:3, therefore Aharoni et al.’s GAME 15 as a cellulose synthase-like protein is the species recited in claim 1.
Regarding argument on the amended recitation of “wherein a bud length of the genetically modified potato kept in a dark place after an end of a post-harvest dormant period is 50% or less relative to a bud length of a genetically unmodified potato”, the argument was not found persuasive since Hartmann et al. teaches genes involved in the biosynthesis of cellulose (cellulose synthase) were found to be induced exclusively in wild-type tubers (Supplemental Tables S1 and S2) (page 786, left paragraph 1). Therefore, someone skilled in the art would screen for changing in bud length and sprouting in the method of creating mutant tuber plant for cellular synthase gene such as CSLM gene as taught by Aharoni et al. and further in view of Liu et al. Furthermore, applicant has compared the bud length to any of unmodified potato wherein any of a unmodified potato would have large diversity in the bud length emergence, which some of them would be sensitive to faster tuber bud production and the modified plant would have 50% or less bud length upon screening.
Furthermore, where a rejection of a claim is based on two or more references, a reply that is limited to what a subset of the applied references teaches or fails to teach, or that fails to address the combined teaching of the applied references may be considered to be an argument that attacks the reference(s) individually. Where an applicant’s reply establishes that each of the applied references fails to teach a limitation and addresses the combined teachings and/or suggestions of the applied prior art, the reply as a whole does not attack the references individually as the phrase is used in Keller and reliance on Keller would not be appropriate. This is because the test for obviousness is what the combined teachings of the references would have suggested to a person having ordinary skill in the art (PHOSITA).”
Summary
No claim is 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.
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/SANTOSH SHARMA/ Examiner, Art Unit 1663
/Amjad Abraham/ SPE, Art Unit 1663
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