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 the Claims
The amendments and arguments filed 11December2025 are acknowledged and have been fully considered. Claims 9, 14-17, 21, 24, 26-34 are canceled. Claims 1-8, 10-13, 18-20, 22-23, 25, 35-37 are pending and examined on the merits herein. Claims 1-5, 7-8, 11-12, 18, 22-23, 25, 35-37 are currently amended. Claims 10, 13 were previously presented. Claims 6, 19-20 are original.
Please note that non-elected claims 14-15, 21, 26-34 (which were withdrawn at the nonfinal dated 11June2025) are now canceled (see claims dated 11December2025).
Priority
Please note the change in priority claim(s) (i.e., Applicant’s petition and Application Data Sheet filed 15December2025 and petition decision dated 23December2025).
Applicant claims the benefit of a prior-filed application under 35 U.S.C. 119 [PCT/EP2020/070347 filed 17July2020] and 35 U.S.C. 120 [PCT/EP2021/070104 filed 19July2021]. Claims 1-8, 10-13, 18-20, 22-23, 25, 35-37 appear to maintain an effective filing date of 17July2020.
Withdrawn Objections and/or Rejections
Objections and/or rejections made of record in the nonfinal office action dated 11December2025 that are not otherwise discussed herein are withdrawn. In particular:
RE ¶ 7: The objection to claim 1 (regarding the recitation of “SEQ ID NO: 42” instead of “SEQ ID NO: 44”) is withdrawn in view of Applicant’s Remarks that:
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RE ¶ 8: The objection to claims 3, 36 (regarding the recitation of “GGC” instead of “GCC”) is withdrawn in view of Applicant’s Remarks that:
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RE ¶ 10: The objection to claim 6 is withdrawn in view of Applicant’s Remarks that:
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RE ¶ 11: The objection to claim 12 is withdrawn in view of the amendments thereto;
RE ¶¶ 12-16: The Indefiniteness rejections are withdrawn in view of the amendments thereto;
RE ¶ 19: The rejection of claims 11-12 for being improperly dependent is withdrawn in view of the amendments to the claims;
RE ¶ 21: The Utility rejection is withdrawn in view of the claim amendments;
and
RE ¶ 22: With respect to deposited seed, please note that Applicant’s representative states the following (Remarks 22December2025):
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.
Drawings
The drawings filed 11December2025 are objected to. Please note that the drawings were objected to (in particular FIGs 2, 3, 4, 7, and 8) in the nonfinal dated 11June2025. The amended drawings filed 11December2025 appear to correct the illegible text issues raised in the nonfinal, but the manner of filing has now raised different objections. Applicant did not submit all figure pages (note the bold text within the form paragraph copied below, which was within the nonfinal action as well). Applicant only submitted the 5 amended figure pages 11December2025 = the 14 pages of figures previously of record (09January2023) is now replaced with just 5 pages. This is believed to be an inadvertent filing error, but nonetheless triggers this new objection because the of record figure pages dated 11December2025 are now mis-numbered and the labels do not correspond to what is described within the specification (e.g., the first figure is now “Fig. 2” and there is no “Fig. 1” as described by the specification).
[Form Paragraph, Copied from Nonfinal →] Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
“SNP” Marker
For clarity of the record, please note that “SNP” as used in this application includes InDels (i.e., “SNP” herein has a different meaning than in the art).1
Claim Objections
Claim 22 REMAINS objected to, and claims 23, 25 are objected to, because of the following informalities: these claims refer to a plant/part having “resistance to ToBRFV”. Whilst “resistance to” is not given a limiting definition in the specification, it is understood (from having reviewed the specification) that this phrase is meant to mean 100% resistance to ToBRFV as well as an improved resistance to ToBRFV. For clarity of the claims, it is recommended that “resistance to” be amended throughout the claims to something like “increased resistance to ToBRFV as compared to a S. lycopersicum plant/part that does not homozygously comprise the mutant Tom2a allele” (see ¶51 on page 11 of the specification). Appropriate correction is required.
Response to Applicant’s Remarks:
As an initial matter, claims 19 and 20 were included in this objection within the Nonfinal dated 11June2025 (¶9 on page 4). Claims 19 and 20 are not amended to address this objection and, upon further review, the Office believes that an amendment on this issue is not necessary (those claims refer to a QTL that “leads to ToBRFV resistance” and not that the plant/part already has ToBRFV resistance = the plants/parts of claims 19 and 20 may comprise the QTL heterozygously and, in that way, be a carrier for the QTL which, when homozygously present, causes ToBRFV resistance).
Applicant asserts that the amendments to claims 5, 16, 19-20, and 22 overcome this objection (Remarks at page 11).
That is true with respect to claims 5 and 16 (claim 16 having been canceled, claim 5 having been amended as suggested), but not true as to claim 22 (and now, as amended, claims 23 and 25). Because claims 22, 23, and 25 refer to plants/parts that are “ToBRFV resistant” (which is understood from the specification to require the homozygous presence of a mutant Tom2a allele characterized by a GGC deletion from positions 312-314 of the nucleic acid sequence SEQ ID NO: 47 and an alanine deletion from position 105 of the amino acid sequence SEQ ID NO: 48), please amend claim 22 to recite “… comprising identifying the homozygous presence of the QTL …” and “… selecting a plant that comprises said QTL homozygously as a ToBRFV resistant plant” and add a line to the claim like “wherein the selected plant exhibits increased resistance to ToBRFV as compared to a Solanum lycopersicum plant or plant part that does not homozygously comprise the QTL”.
Claim 1 is objected to because of the following informalities: please amend the claim as follows “… 95% sequence identity to SEQ ID NO: 45 has retained …” (note is needed at two locations). Appropriate correction is required.
Claim 2 is objected to because of the following informalities: although claim 2 refers back to claim 1, claim 2 does not say that the Tom2a sequence “retains a GGC deletion at positions corresponding to 312-314 of SEQ ID NO: 47”. Based on Applicant’s arguments of record 11December2025, this is assumed to be an oversight and is, therefore, raised here as an objection. Appropriate correction is required.
Claim 3 is objected to because of the following informalities: the phrase “comprising the Tom2a sequence having at least 95% sequence identity to SEQ ID NO: 45,” is unnecessary and should be removed from the claim (i.e., just start the claim with a “wherein” clause). Appropriate correction is required.
Claim 5 is objected to because of the following informalities: the language used at claim 5 is inconsistent with claim 1 (to which it refers) in several ways:
Claim 5 recites homozygously comprise the mutant Tom2a allele whereas claim 1 says that it is the QTL which is homozygously comprised,
Claim 5 says “wherein the QTL is present homozygously” but that is already stated in claim 1 (= this phrase is redundant at claim 5 and, in any event, inconsistent with the later phrase in claim 5 stating that it is the mutant Tom2a allele which is homozygously present)
Please pick either the QTL is homozygously present or the mutant Tom2a allele is homozygously present, then update the claims (including claims 1 and 5) accordingly. To be clear, it is understood from the specification that there is no technical difference between these phrases because the sequence modifications of these claims are within the mutant Tom2a allele which is within the QTL on chromosome 8 between SEQ ID NOs: 1 and 42). Note that if the “mutant Tom2a allele” language is preferred by Applicant, claim 1 currently does not say “mutant”, hence the antecedent basis issue raised below. Please also note the proposed claims at the bottom of this action.
Appropriate correction is required.
Claims 5 and 35 are objected to because of the following informalities: “plant/part” should be “plant or plant part”. Appropriate correction is required.
Claim 11 is objected to because of the following informalities: this claim recites “seed of, or from, or that produces the plant of claim 1”. It is not clear what “seed of” means in this context and how it is neither “from” the plant of claim 1 nor a seed “that produces the plant of claim 1”. Please delete the “seed of” language from claim 11. Appropriate correction is required.
Claims 36 and 37 are objected to because of the following informalities: (1) these claims are missing the following phrase “… conversion at the position corresponding to position “ and (2) parts i) and 1) of these claims, respectively, are already required by claim 35, to which they refer, and should therefore be removed for clarity. Also (3) if parts i) and 1) are maintained by Applicant, then please clarify the claim language because it is confusing to have part i)/1) not optional and then try to say that any one of the next three parts are optional—reciting an “optionally” phrase in the alternative is confusing. Note that claim 37 refers to an amino acid deletion which, as raised below in the indefiniteness section, the Office believes should be deleted but if it is not, in any event claim 37 does not currently say that the QTL “encodes a deletion of Ala…” (i.e., the word “encodes” is missing). Appropriate correction is required. Please see the proposed claim amendments at the bottom of this action (especially new claim 39).
Claim Objections
Applicant is advised that should claim 19 be found allowable, claim 20 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Applicant is advised that should claim 23 be found allowable, claim 25 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
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.
Claim 5 is 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.
The following phrase “the mutant Tom2a allele” lacks antecedent basis in the claim.
Claims 18, 23, 25 is 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.
These claims refer to an “InDel” within SEQ ID NO: 28 or a “SNP” within SEQ ID NOs: 26, 43, or 44. First, there is no limiting definition of what constitutes the supposed “InDel” or “SNP” which makes the meaning of these terms unclear. At claims 23 and 25, for example, the phrase is “the InDel presented in SEQ ID NO: 28”—one is left wondering what sequence(s) within SEQ ID NO: 28 that Applicant considers an “InDel” and wondering whether it is just one or multiple? Neither of which are supported by this specification. Second, the referenced sequences are already mutated/modified, so it is unclear if Applicant is now saying that the mutated/modified sequence is the “InDel”/”SNP” or if the wild type sequence (i.e., that present within SEQ ID NO: 47) is the “InDel”/”SNP”. Third, especially because the Tom2a mutation described by this specification is a deletion (a GGC deletion at the position corresponding to 312-314 of SEQ ID NO: 47, which results in the mutant/modified marker sequence SEQ ID NO: 28); claiming an “InDel” at position 101 of SEQ ID NO: 28 does not make sense because there is no insertion mutation/modification within SEQ ID NO: 28 (just a deletion) and SEQ ID NO: 28 is already mutated/modified (= the sequences at and around position 101 are those resulting from a deletion and so it does not make sense to say there is an “InDel” at position 101 without at least saying what the comparative wild type sequence is—as written, someone would have to do a sequence alignment using SEQ ID NOs: 28 and 47 (or the complement thereof) to know what “InDel” produces SEQ ID NO: 28 and, even then, it is only a deletion and not an insertion). Please delete the “InDel” and “SNP” language from these claims and just recite the specific nucleic acid changes (as is suggested within the proposed claim amendments below).
Claims 19-20 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.
These claims refer back to claim 16, which is now canceled. It is assumed that these claims were intended to refer back to claim 18.
Claims 22, 35, 37 (therefore, claims 23, 25, 36 which refer thereto without correcting the issue) 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.
Claims 22, 35, 37 regard determining whether a particular nucleic acid is present or absent (namely, a GGC deletion at the position corresponding to 312-314 of SEQ ID NO: 47) but these claims also now recite that identifying includes identification of an amino acid deletion (a deletion of alanine at the position corresponding to 105 of SEQ ID NO: 48). It does not make sense to refer to amino acids in these method claims, please delete such references. For exemplary claim language, see the proposed claims below.
Claims 23 and 25 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.
Claims 23 and 25 are rejected for having an unclear format. In particular, both recite language that make it unclear whether a Markush group is being claimed or not (if yes, it is in improper format). At Claim 23, the claim recites “a marker selected from the group consisting of … and optionally … or SEQ ID NO: 44” and at claim 25, the claim recites “a marker selected from the group consisting of the … and the SNP … and SEQ ID NO: 44”. Neither of which is in proper Markush group format nor clear as to what, exactly, is within the claims scope. The use of “optionally” and “or” at claim 23 are problematic and the use of “and” twice in claim 25 is problematic. Please note that claim 22, to which both claims 23 and 25 refer, already says that a deletion of GGC (at the position corresponding to 312-314 of SEQ ID NO: 47) is present; so claims 23 and 25 are further unclear because they seem to suggest that the marker is just SEQ ID NO: 26, 43, or 44 (no longer requiring the GGC deletion?) which is not supported by the specification or claim 22.
Claims 35-37 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.
Claim 35 is indefinite due to several unclear recitations (= claims 36 and 37 are also indefinite because they refer thereto without correcting the issues). The problems within claim 35 are elucidated by at least two things: (1) the part ii) does not say that the Tom2a sequence “retains” the GGC deletion (a structural feature which is already required by part a) of the claim, recited above) and (2) it is not clear whether the last paragraph of the claim is optional or not (note that parts c) and d) above it recite “optionally”). Taken together, there are multiple formatting issues within claim 35 that make the scope of the claim altogether unclear. Please see the proposed claim amendments below for how this claim may be cleaned up. Further, with respect to the format of claims 36 and 37, Applicant has added “optionally” statements (presumptively to get around the Written Description/Utility issues raised of record) but has not clearly updated the recitations of “and” as well as “or”. As currently written, claims 36 and 37 seem to suggest that the GGC deletion (which encodes the Alanine deletion) is one of four options (note the use of “or” between the parts) which contradicts what is believed to be required by claim 35, to which claims 36-37 refer (note part a) of claim 35 already requires the GGC deletion be identified). Taken together, the formatting of claims 36 and 37 makes the meaning of the claims unclear. Please see the proposed claim amendments below.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 18 REMAINS rejected under 35 U.S.C. 101 because the claimed invention is directed toward a law of nature without significantly more. MPEP § 2106(III).
Step 1:
Marker claim 18 recites a marker that may be present within any environment (the claimed markers do not even need to be isolated)—it would be reasonable to interpret these claims as being directed toward information (a sequence) which does not fall into a statutory category of invention and, for that reason alone, means marker claim 18 is not patent eligible. To the extent marker claim 18 is interpreted as being directed toward isolated marker sequences (and, therefore, a composition of matter), they still are not patent eligible because the specification explains that these markers (as well as the Tom2a loci and the QTL within which it exists) are all naturally present within Solanum pimpinellifolium plants/parts2 which is a naturally-occurring Solanum species that comprises various degrees of ToBRFV resistance3.
Step 2A, Prong One:
Pursuant to the above discussion, claim 18 may be interpreted as being directed toward a naturally occurring sequence. Therefore, these claims recite a law of nature. MPEP § 2106.04, especially §2106.04(II)(A)(1).
Step 2A, Prong Two:
Because this claim does not recite additional elements, this claim does not (and, in fact, cannot) recite features that “integrate the judicial exception [law of nature] into a practical application”. Please be reminded that the “identifying” and resistance phenotype text in claims 16-18 are reasonably interpreted as non-limiting, intended uses of the claimed markers. MPEP § 2106.04, especially §2106.04(II)(A)(2).
Step 2B:
The claim does not recite additional elements and, therefore, does not (and, in fact, cannot) recite additional elements that “amount to significantly more than the judicial exception [law of nature]”.
For these reasons, and based on the current record, claim 18 REMAINS directed toward subject matter that is not eligible for patenting.
Response to Applicant’s Remarks:
As an initial matter, claims 11-12 and 16-17 are removed from this rejection due to claim amendments (claims 11-12 now specify Solanum lycopersicum and claims 16-17 are canceled).
Applicant does not make any arguments specifically for the content of claim 18. While claim 18 is amended, the structural/sequence elements of the claim are understood to be those which are found within a naturally occurring Solanum pimpinellifolium plant or plant part and the “for identifying” clause of the claim is a non-limiting intended use. For at least these reasons, Applicant’s amendments to the claims and Remarks are unpersuasive and claim 18 remains rejected.
As said within Issue (C) of the of record Written Description rejection (Nonfinal bridging pages 19-20), the Office still does not see a path toward patentability for claim 18.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-5, 7-8, 10-13, and 18 REMAIN rejected, and claim 6 is rejected, under 35 U.S.C. 102(a)(1) as being anticipated by Applicant’s own HAMELINK et al. (WO2019110130 published 13June2019 of record IDS 09January2023).
As an initial matter, claims 9, 16-17 are removed from this rejected because they are now canceled. Claim 6 is added to this rejection in view of Applicant’s Remarks regarding the objection to claim 6 (see ¶10 at page 4 of the Nonfinal dated 11June2025). With Applicant’s Remarks, copied below for completeness, Applicant is arguing that claim 6 is not limited to a plant represented by the seed deposited under NCIMB Accession Number 43637, but is truly directed toward any plant [homozygously] comprising the QTP which is also found within the deposited seed (i.e., Applicant argues that the QTL of claim 6 is not obtained from the deposited seed). Because the QTL of claim 6 is now understood to merely have the same structure/sequence as that found within the seed deposited with Accession Number 43637, claim 6 is now added to this rejection.
The specification explains that the QTL, Tom2a allele, and markers of these claims originated from Solanum pimpinellifolium GNL3951.4 The specification also explains that the S. lycopersicum plants/parts of these claims (which comprise the QTL/Tom2a allele/marker(s)) was obtained by crossing Solanum pimpinellifolium GNL3951 with Applicant’s internal S. lycopersicum line “TB2”.5
HAMELINK et al. teach S. pimpinellifolium GNL3951 [claims 18] and crossing it with Applicant’s internal S. lycopersicum line “TB2” as well as S. lycopersicum plants/parts comprising a QTL from GNL3951 that leads to TBRFV resistance6 [claims 1-8, 10-13].
Absent evidence from Applicant, it appears as though the products/structures taught by HAMELINK et al. anticipate these claims. Importantly, while HAMELINK et al. does not reference a QTL/Tom2a allele/marker on chromosome 8 of a S. lycopersicum plant/part (originating from a S. pimpinellifolium plant/part); there is nothing of record to show that this feature was not inherently present within the products/structures taught by HAMELINK et al.
Regarding claim 6, there is no information of record to show that the QTL of claim 6 is any different (structurally) than that taught by HAMELINK et al. (including, perhaps, the QTL within the deposited seeds referenced by HAMELINK et al.7; though HAMELINK et al. does not reference an accession number NCIMB 43637. As said of record within the Nonfinal dated 11June2025, HAMELINK et al. is Applicant’s publication and, because the Office has limited fact-finding abilities, Applicant is in the best position to know and evidence whether or not the subject matter taught by HAMELINK et al. truly anticipates these claims.
Applicant is encouraged to use declaration practice for providing evidence to show HAMELINK et al. does not anticipate these claims. Please note that at least one person (KALISVAART, J.) is listed as an inventor on BOTH this application and HAMELINK et al. (= a declaration by that person should be considered). To that end, Applicant is reminded of their “Duty of Disclosure, Candor, and Good Faith” (see 37 C.F.R. § 1.56 and MPEP § 2001).
Assuming no persuasive evidence is provided for overcoming this anticipation rejection, Applicant should consider canceling product claims and only pursuing method claims.
Response to Applicant’s Remarks:
In Remarks only, Applicant asserts that HAMELINK et al. “does not teach or disclose the homozygous presence of the QTL” (Remarks at page 18) and, therefore, Applicant asserts that HAMELINK et al. does not teach every element of these claims and cannot be an anticipatory reference.
This is not persuasive because, according to the specification, ToBRFV resistance is present when the QTL is homozygously present. So, absent evidence to the contrary (such as declaration evidence), the fact that ToBRFV resistance is taught by HAMELINK et al. suggests that the QTL is homozygously present (otherwise resistance would not be taught). And, in any event, an argument regarding homozygosity is not relevant to the marker of claim 18.
Claim Rejections - 35 USC § 112- Written Description
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 5, 19-20, 22-23, 25, 35, 36 (parts ii-iv), 37 (parts 2-4) 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 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.
As amended 11December2025, only claims 22-23 and 25 perpetuate Issues (A) and (B) because those claims do not state that the QTL is homozygously present. The amendments to claims 5, 19-20, 35-37 are sufficient to overcome this rejection and all of Issues (A), (B), (C) (as applied to those claims in the Nonfinal dated 11June2025).
*Due to the nature of this specification and these claims, the claimed subject matter will be discussed after a summary of what is described by the specification and prior art.*
The specification describes a mutant Tom2a allele comprising SEQ ID NO: 45 (encoding SEQ ID NO: 468) which encodes a Tom2a protein with reduced function9 and that, when homozygously present (due to it being recessive10) on chromosome 8 within a Solanum lycopersicum plant, confers an increased resistance to Tomato brown rugose fruit virus (ToBRFV) as compared to a S. lycopersicum plant that does not comprise the allele homozygously on chromosome 811. Representative seed of one such S. lycopersicum plant has also been deposited.12
Further to the Indefiniteness Rejection Above Regarding SEQ ID NO: 30, Some Context: There appear to be two mutations identified by Applicant which render Tom2a non-functional: (1) having a GCC deletion at nucleotides 312-314 of the wild type Tom2a coding sequence SEQ ID NO: 47 which encodes a deletion of the alanine residue at position 105 of the wild type Tom2a amino acid sequence SEQ ID NO: 4813 and (2) a G deletion14. The specification describes several, what it calls, “SNP” marker sequences for (supposedly) identifying the QTL on chromosome 8 which comprises this mutant Tom2a allele.15 Amongst those, is the sequence SEQ ID NO: 28 which is a marker sequence specific for the (1) GCC deletion at nucleotides 312-314 of the sequence SEQ ID NO 4716 (which encodes/causes an Alanine deletion at position 105 of the amino acid sequence SEQ ID NO: 48). Also, the specification describes marker sequence SEQ ID NO: 30 which is specific for (2) “a deletion of G, as found on positions 101-103 of SEQ ID NO: 30”. For the sake of a clear record, the Office does not see (2) a G deletion reflected in SEQ ID NOs: 45 and 46 (i.e., the full length, mutant Tom2a sequence) (e.g., there are no gaps representing a G deletion in the of record alignments of SEQ ID NO: 45 to 4717 or of SEQ ID NO: 45 to 4818). It is also noted that a G deletion is not specifically claimed (see claims 3-4 and 36-37). So, it is not clear to the Office whether there is a mistake in the sequences of record or whether a G deletion (i.e., use of the marker sequence SEQ ID NO: 30) is now known to be irrelevant to the claimed invention. Whatever the reason for this discrepancy, please correct and/or clarify the record as to the “G deletion” Tom2a mutant and marker sequence SEQ ID NO: 30. Due to the fact that these claims recite SEQ ID NO: 45 and SEQ ID NO: 45 does not appear to comprise a “G deletion”, the (2) G deletion mutant discussed at ¶¶129-130 of the specification (pages 29-30) will not be discussed further (= the Written Description analysis will resume on the basis of the (1) GCC deletion being the sole mutation described within the specification as effectuating a non-functional Tom2a).
For the reasons set forth in the “context” section above, the specification (as it pertains to the claimed sequences SEQ ID NOs: 45 and 46) is understood to describe one mutation that effectuations a non-functional Tom2a allele: that having a GCC deletion at nucleotides 312-314 of the wild type Tom2a coding sequence SEQ ID NO: 47 (which encodes a deletion of the alanine residue at position 105 of the wild type Tom2a amino acid sequence SEQ ID NO: 4819). The specification describes several, what it calls, “SNP” marker sequences for (supposedly) identifying the QTL on chromosome 8 which comprises this mutant Tom2a allele.20 Amongst those, is the sequence SEQ ID NO: 28 which is a marker sequence specific for the GCC deletion at nucleotides 312-314 of the sequence SEQ ID NO 4721 (which encodes/causes an Alanine deletion at position 105 of the amino acid sequence SEQ ID NO: 48). To be clear, whilst many other “SNP” markers are described by this specification (SEQ ID NOs: 1-44 at Table 422), the specification evidences that only a sub-set of SEQ ID NOs: 1-44 are tightly linked to the Tom2a loci because recombinations occurred on both sides of the Tom2a loci23 when a marker sub-set was analyzed (which appears to be the region between SEQ ID NO: 23 and SEQ ID NO: 34 per ¶139 on page 32 and FIG. 4—please note the objection to FIG. 4 herein above—please also note that seven putative genes are believed to be present between marker sequences SEQ ID NO: 23 and 34,24 one of which was shown to be Tom2a). While it is not clear from the specification of record which, specific, marker sequences are actually tightly linked to the Tom2a loci, the material information for these claims is instead which marker(s) sequences is/are specific for a mutant Tom2a because it is the mutant Tom2a gene which correlates to increased ToBRFV resistance. Further to the comments herein above, only one marker sequence appears to be specific for a mutant Tom2a (that marker being SEQ ID NO: 28). To be clear, other markers which are tightly linked to the Tom2a loci would only tell a skilled artisan whether a Tom2a allele is located at a particular position on chromosome 8—those other markers (i.e., those other than SEQ ID NO: 28) cannot distinguish between a wild type Tom2a allele and a mutant Tom2a allele (therefore, they alone are not useful for identifying whether a plant has increased resistance to ToBRFV). It appears as though at least SEQ ID NO: 28 must be present to signify that a mutant Tom2a allele is present and, when SEQ ID NO: 28 is homozygously present within a S. lycopersicum plant, that the plant has an increased resistance to ToBRFV.
The prior art does not appear to supplement the specification at least because the prior art does not appear to teach the specific sequences of these claims (especially in the context of a S. lycopersicum plant and ToBRFV resistance).
Issues (A) & (B):
Claims 22-23, 25 are now amended (11December2025) to recite particular mutant Tom2a structures for use in the “identifying” step, but these claims still do not say that the QTL is homozygously present . It is understood that a mutant, non-functional Tom2a allele must be homozygously present to confer increased ToBRFV resistance onto a S. lycopersicum plant.
It would be remedial of these Issues (A) and (B), to amend claim 22 to something like “… comprising identifying the homozygous presence of the QTL …” and “… selecting a plant that comprises said QTL homozygously as a ToBRFV resistant plant” and adding a line to the claim like “wherein the selected plant exhibits increased resistance to ToBRFV as compared to a Solanum lycopersicum plant or plant part that does not homozygously comprise the QTL”. Please also amend claim 23 to something like “… wherein identifying the homozygous presence of the QTL ….” and amend claim 25 to something like “… wherein identifying the homozygous presence of the QTL ….”
Without more from Applicant, a skilled artisan at the time this application was filed would not reasonably believe that Applicant was in possession of the full scope of subject matter being claimed. Please see the individualized suggestions for each of Issues A-D in replying to this rejection.
Response to Applicant’s Remarks:
Applicant asserts that the claims as amended 11December2025 are adequately described and, therefore, this rejection may be withdrawn.
That is true in-part, please amend claims 22-23 and 25 to specify that the QTL is homozygously present.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-5, 7-8, 10-13, 18-20, 22-23, 25, 35-37 REMAIN provisionally rejected, and claim 6 is provisionally rejected, on the ground of nonstatutory double patenting as being unpatentable over claims 1-7, 9-18, 23-25 of copending Application No. 18774411 (Attny. Dkt. No. Y7954-00614, published as US20250008903). Although the claims at issue are not identical, they do not appear to be patentably distinct from each other.
As an initial matter, claims 9, 16-17, 24 are removed from this rejected because they are now canceled. Claim 6 is added to this rejection in view of Applicant’s Remarks regarding the objection to claim 6 (see ¶10 at page 4 of the Nonfinal dated 11June2025). With Applicant’s Remarks, copied below for completeness, Applicant is arguing that claim 6 is not limited to a plant represented by the seed deposited under NCIMB Accession Number 43637, but is truly directed toward any plant [homozygously] comprising the QTP which is also found within the deposited seed (i.e., Applicant argues that the QTL of claim 6 is not obtained from the deposited seed). Because the QTL of claim 6 is now understood to merely have the same structure/sequence as that found within the seed deposited with Accession Number 43637, claim 6 is now added to this rejection.
The claims of application number 18774411 are directed toward Solanum lycopersicum plants/parts comprising a mutant Tom2a gene or protein and certain methods for obtaining one such plant/part. The claims of application number 18774411 broadly refer to Tom2a genes or proteins with as little as 70% sequence identity to the sequences references therein. Please also note that while the claims of 18774411 refer to Cucummis plants/parts, the claims also refer to S. lycopersicum plants/parts. On their face, and absent evidence to the contrary from Applicant, the claimed subject matter of co-pending application 18774411 appear to teach or suggest that of claims 1-5, 7-8, 9-13, 16-20, 22-25, 35-37 of this application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Applicant’s Remarks:
Applicant asserts that this provisional rejection because, according to Applicant, this application has an earlier effective filing date than 18774411 and that MPEP § 804(I)(B)1(b)(i) call for a withdrawal in this scenario (Remarks at page 25).
Applicant is incorrect about the cited MPEP section—ignoring the bit about both applications having a provisional double patenting rejection, withdrawal would still only be appropriate if the claims of this application are otherwise in condition for allowance (which is clearly not the case here per the content of this action).
Conclusion
Applicant should consider pursuing claims like the following (with “Previously Canceled” statuses being used to distinguish claims that the Office proposes are canceled from those that were already canceled within the claims dated 11December2025). Please note that where the claims discuss a marker sequence or QTL (which are polynucleotide sequences), it is suggested that references to the amino acid sequence SEQ ID NO: 48 be removed (it is understood that a GGC deletion at 312-314 of polynucleotide sequence SEQ ID NO: 47 causes/encodes an alanine deletion at position 105 of the amino acid sequence SEQ ID NO: 48. Also, and further to the objections and indefiniteness issues raised above, the Office recommends substituting “SNP in SEQ ID NO: 26, SEQ ID NO: 43, or SEQ ID NO: 44” language at claim 23 with reference to the actual changes therein (see ¶39 at page 9 of the specification and claim 36). Further, it is understood that SEQ ID NOs: 45 and 47 are both mutant minus strands comprising the “GGC deletion at positions corresponding to 312-314 of SEQ ID NO: 47”, so it is recommended that claim 35 be simplified to just refer to a QTL homozygously comprising [the mutant Tom2a characterized by] “the presence of SEQ ID NO: 28 and/or … a GGC deletion at the position corresponding to 312-314 of SEQ ID NO: 47.” Finally, the subject matter of present claims 36-37 is (meant to be) captured within new claim 39 (written in a manner that addresses the objections and rejections raised herein above). Bold typeface is used to more easily identify changes.
AMENDMENTS TO THE CLAIMS:
1.-8. (Canceled)
9. (Previously Canceled)
10.-13. (Canceled)
14.-17. (Previously Canceled)
18. (Canceled)
19. (Currently Amended) A method for identifying a QTL on chromosome 8 that leads to Tomato brown rugose fruit virus (ToBRFV) resistance in a plant, , comprising identifying a marker in the plant, wherein
the plant is a Solanum lycopersicum (S. lycopersicum) plant, or a Solanum pimpinellifolium plant, or a plant of another Solanum species that is sexually compatible with S. lycopersicum; and
the marker is located between SEQ ID NO: 1 and SEQ ID NO: 42, and comprises SEQ ID NO: 28 and/or a GGC deletion at the position corresponding to positions 312-314 of SEQ ID NO: 47.
20. (Canceled)
21. (Previously Canceled)
22. (Currently Amended) A method for selecting a ToBRFV resistant planthomozygous presence of a[[the]] QTL on chromosome 8 of a plant, and selecting the[[a]] plant that homozygously comprises said QTL as a ToBRFV resistant plant, wherein
the plant is a Solanum lycopersicum (S. lycopersicum) plant, or a Solanum pimpinellifolium plant, or a plant of another Solanum species that is sexually compatible with S. lycopersicum; and
identifying comprises identification within the QTL of the presence of SEQ ID NO: 28 and/or identification within the QTL of a GGC deletion at the position corresponding to positions 312-314 of SEQ ID NO: 47
23. (Currently Amended) The method of claim 22, wherein identifying further comprises identification within the QTL of the presence of a guanine (G) at the position corresponding to 559 of SEQ ID NO: 47, an adenine (A) at the position corresponding to 673 of SEQ ID NO: 47, and/or a guanine (G) at the position corresponding to 844 of SEQ ID NO: 47
24. (Previously Canceled)
25. (Canceled)
26.-34. (Previously Canceled)
35.-37. (Canceled
38. (New) A method of selecting a Solanum lycopersicum plant or plant part that exhibits increased resistance to ToBRFV, comprising:
a) identifying in a Solanum lycopersicum plant or plant part by genetic analysis the homozygous presence of a QTL on chromosome 8 located between SEQ ID NO: 1 and SEQ ID NO: 42, wherein identifying comprises identification within the QTL of the presence of SEQ ID NO: 28, and/or identification within the QTL of a GGC deletion at the position corresponding to positions 312-314 of SEQ ID NO: 47; and
b) selecting a plant or plant part from a) that comprises said QTL homozygously, optionally testing the selected plant or plant part for increased resistance to ToBRFV as compared to a Solanum lycopersicum plant or plant part that does not comprise said QTL homozygously, wherein the selected plant or plant part does exhibit increased resistance to ToBRFV as compared to a Solanum lycopersicum plant or plant part that does not comprise said QTL homozygously.
39. (New) The method of claim 38, wherein identifying further comprises identification within the QTL of the presence of a guanine (G) at the position corresponding to 559 of SEQ ID NO: 47, an adenine (A) at the position corresponding to 673 of SEQ ID NO: 47, and/or a guanine (G) at the position corresponding to 844 of SEQ ID NO: 47.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Rebecca STEPHENS whose telephone number is (571)272-0070. The examiner can normally be reached Monday through Friday 8:30-4:30.
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/REBECCA STEPHENS/Examiner, Art Unit 1663
/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
1 ¶130 on page 30 of the specification.
2 See the language of claims 8, 16, 19, 20, 22 which all explicitly state that these markers/Tom2a allele/QTL are present within a S. pimpinellifolium plant/part as well as ¶¶26-32 on pages 5-7 of the specification explaining that Applicant introgressed the markers/Tom2a allele/QTL into S. lycopersicum from S. pimpinellifolium.
3 See generally KABAS et al. “Screening of wild tomato species and interspecific hybrids for resistance/tolerance to Tomato brown rugose fruit virus (ToBRFV)” 2022 Chilean J. Agri. Res. 82(1):189-196.
4 ¶22 on page 5 (regarding FIG. 5), ¶124 on page 26, ¶¶134-138 on pages 31-32 of the specification
5 ¶124 on page 26 and ¶136 on page 31 of the specification.
6 HAMELINK et al. at lines 21-27 on page 2, lines 5-11 on page 5, lines 32-35 on page 19, and page 20 as well as claims 1-9 on pages 23-24.
7 See HAMELINK et al. at lines 5-11 on page 5.
8 See ¶¶22-23 on page 5 and FIGs. 5-6 of the specification. Noting that the wild type sequence of the Tom2a gene is SEQ ID NO: 47 of this application (encoding SEQ ID NO: 48). See ¶36 on page 8 of the specification.
9 ¶¶44-45 on page 10 of the specification.
10 ¶51 on page 11 of the specification.
11 ¶127 on page 27 of the specification.
12 ¶¶15-16 on pages 4-5 of the specification.
13 ¶¶44-45 on page 10, ¶¶129-130 on pages 29-30, ¶¶26-32 on pages 5-7 of the specification; see also Result 1 of the “47.rapbm” sequence search results file of record showing that position 105 of SEQ ID NO: 48 aligns to positions 313-315 of SEQ ID NO: 47.
14 ¶¶129-130 on pages 29-30, ¶¶26-32 on pages 5-7 of the specification.
15 See, e.g., Table 4 on pages 27-29 as well as discussions of Table 4 and the “SNP” sequences listed therein.
16 ¶39 on page 9 of the specification. See also Table 4 at ¶128 on pages 27-29 as well as ¶¶129-130 on pages 29-30 and ¶¶26-32 on pages 5-7.
17 See the “45.rnpbm” file aligning nucleotide sequences.
18 See the “45.rapbm” file aligning nucleotide sequence SEQ ID NO: 45 to amino acid sequences.
19 ¶¶44-45 on page 10, ¶¶129-130 on pages 29-30, ¶¶26-32 on pages 5-7 of the specification; see also Result 1 of the “47.rapbm” sequence search results file of record showing that position 105 of SEQ ID NO: 48 aligns to positions 313-315 of SEQ ID NO: 47.
20 See, e.g., Table 4 on pages 27-29 as well as discussions of Table 4 and the “SNP” sequences listed therein.
21 ¶39 on page 9 of the specification. See also Table 4 at ¶128 on pages 27-29 as well as ¶¶129-130 on pages 29-30 and ¶¶26-32 on pages 5-7.
22 ¶128 on pages 27-29 of the specification.
23 ¶¶139-142 on pages 32-33 of the specification.
24 ¶139 on page 32 of the specification.