Detailed Action
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim 3 is cancelled.
Claims 1, 4-12, and 14-21 are pending.
Claims 17-18 are withdrawn.
Claims 1, 4-12, 14-16 and 19-21 are examined.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 3/17/2026 has been entered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Applicant refers to sequences AT3G07590 (page 29, paragraph 1) and AT4G02840 (Table 1; page 29, paragraph 1) without a sequence identifier assigned to these sequences. It is noted that the two place in the Specification referring to AT4G02840 appear to be conflicting. In Table 1 it appears AT4G02840 is referring to the Arabidopsis wildtype SmD1b gene and in page 29, paragraph 1, it appears AT4G02840 is referring to a mutant smd1b.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
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 1, 4-12, 14-16 and 19 remain rejected and claims 20 and 21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Due to Applicant’s amendments of the claims, the rejection is modified from the rejection set forth in the Office action mailed 11/20/2025.
Applicant claims a plant comprising an SmD1 allele encoding an SmD1 protein with at least 90% identity to SEQ ID NO: 1, wherein said SmD1 protein comprises a missense mutation at a position corresponding to amino acid position 14 of SEQ ID NO: 1, resulting in a modified SmD1 protein conferring improved nematode resistance against nematodes of the genus Meloidogyne. SEQ ID NO: 1 comprises 114 amino acids. Sequences comprising at least 90% identity to SEQ ID NO: 1 include sequences with 11 amino acids changed at any position throughout the sequence.
Claim 4 is drawn to the modified SmD1 protein comprising a threonine to isoleucine substitution at a position corresponding to amino acid position 14 of SEQ ID NO: 1.
Claim 5 is drawn to the SmD1 allele being obtained by mutagenesis.
Claim 6 is drawn to the plant being selected from a Markush group of plant species.
Claim 7 is drawn to the plant being an inbred, dihaploid or hybrid plant.
Claim 8 is drawn to the plant being a rootstock.
Claim 9 is drawn to the plant comprising two copies of the SmD1 allele.
Claim 10 is drawn to the protein conferring improved resistance against Meloidogyne incognita, Meloidogyne arenaria, Meloidogyne hapla, Meloidogyne enterolobii and Meloidogyne javanica.
Claim 11 is drawn to the plant being Solanum lycopersicum.
Claim 12 is drawn to the plant of claim 11 wherein the modified SmD1 protein has an amino acid sequence of SEQ ID NO: 2.
Claim 14 is drawn to a plant part of claim 1 comprising the SmD1 allele.
Claim 15 is drawn to a seed that produces the plant of claim 1.
Claim 16 is drawn to a method of improving nematode resistance against nematodes from the genus Meloidogyne in a plant comprising selecting a mutant plant comprising a modified SmD1 allele encoding an SmD1 protein with a missense mutation at a position corresponding to amino acid position 14 of SEQ ID NO: 1.
Claim 19 is drawn to the plant of claim 1 being a pepper plant.
Claim 20 is drawn to the nematode of claim 1 being Meloidogyne incognita.
Claim 21 is drawn to the plant of claim 20 being a tomato plant.
Applicant describes a yeast two-hybrid experiment using the effector MiEFF18 from nematode Meloidogyne incognita to observe whether the plant protein SmD1 is a potential target of the nematode effector. Applicant describes SEQ ID NO: 1 and 3 are tomato SmD1 genes (Sl06g084310.2.1 and Sl09g064660.2.1, respectively) interacting with the effector. Applicant describes SEQ ID NO: 4, the SmD1b protein from Arabidopsis gene also interacting with the effector. Applicant describes the first 108 amino acids of the SmD1 protein interacting with the nematode effector. Page 28.
Applicant describes obtaining smd1a (At3G07590) and smd1b (At4G02840) mutant Arabidopsis plants and observing that smd1b is less susceptible to M. incognita compared to the wild-type or the smd1a mutant. Page 29, paragraph 1.
Applicant describes Nicotiana benthamiana plants with silenced SmD1 genes were significantly less susceptible to M. incognita compared to a control plant. Page 29, paragraph 2.
Applicant describes tomato plants with silenced SmD1 genes were significantly less susceptible to M. incognita compared to a control plant but had unfavorable growth characteristics otherwise. Page 29, paragraph 3. Applicant describes generating mutant tomato plants using EMS screened in a tilling approach to identify plants with a modified SmD1 gene resulting in a missense mutation of the protein. Applicant describes one tomato line with a missense mutation in its SmD1b gene, line #123, 18TEP250123, homozygous for the mutation, comprised a missense mutation at position 14 of SEQ ID NO: 1 (T14I) wherein the SmD1b mutant allele comprises an ACT[Wingdings font/0xE0]ATT codon. Applicant describes this line was significantly less susceptible to M. incognita compared to a control plant. Applicant describes 18TEP250123 is an ancestor plant of deposited line 19TEP250122. Page 30.
Applicant does not describe a representative number of species across the claimed genus of SmD1 alleles with 90% identity to SEQ ID NO: 1 comprising a missense mutation at a position corresponding to amino acid positions 14 of SEQ ID NO: 1 conferring improved nematode resistance to any species of nematode of the genus Meloidogyne in any species of plant other than tomato. It is not clear what the smd1b mutation observed as conferring reduced nematode susceptibility in Arabidopsis comprised (Page 29, paragraph 1), especially considering that Applicant appears to describe the smd1b mutant by the same name as the SmD1b gene (Table 1). It Is not clear what the mutation of the Smd1 gene in Nicotiana benthamiana comprises (Page 29, paragraph 3 and 4). Applicant does not describe nematode resistance conferred when the modification is heterozygous. Applicant does not describe resistance to any species of nematode other than M. incognita. Applicant has not described a structure which confers the claimed function across the claimed genera of modified proteins, plants comprising the protein and nematodes to which resistance is conferred.
Elvira-Matelot (Elvira-Matelot, et al. 2016. The Plant Cell. 28(2):426-438) teaches identification of smd1b in a genetic screen for PTGS deficiency, revealing involvement of SmD1 in post translational gene silencing (PTGS) in Arabidopsis (Abstract). Elvira-Matelot teaches identification of SmD1 from the Arabidopsis genome comprising at least 42 genes from the Sm family, few of which have been characterized (page 427, paragraph bridging left and right columns). Elvira-Matelot teaches that mutations in RNA quality control (RQC) factors restore PTGS in smd1b while the double mutant of sbd1b and the RQC mtr4 is embryo-lethal (abstract). Elvira-Matelot teaches that SmD1 has a diverse range of functions in the regulation of gene expression. Elvira-Matelot is silent regarding the role of SmD1 in nematode resistance in Arabidopsis or other plants and the effect of missense mutations in SmD1 other than that a smd1a and smd1b double mutant is embryo-lethal (Abstract).
Poraty-Gavra (Poraty-Gavra et al. WO2013179211) teaches SEQ ID NO: 7129, which shares 94.7% identity and is not characterized as an SmD1 protein. See alignment below.
Given the breadth of the genera encompassed by the claims, the described species are not sufficiently representative. The lack of written description provided by Applicant is not cured by the teachings in the prior art. Elvira-Matelot teaches SmD1 has a diverse range of functions and is silent regarding knowledge of the known structures to the claimed phenotype. The lack of representative species described by Applicant and teachings of Elvira-Matelot confirm that there is no structure-function connection between nematode resistance and missense mutations in the SmD1 encoding sequence such that one of ordinary skill in the art would be able to recognize which members of the claimed genus of modified proteins would confer improved resistance to any nematode nor any nematode from the genus Meloidogyne nor to any plant species. It is therefore unclear whether the described embodiments would result in the claimed function across these genera.
Therefore, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that Applicant was in possession of the invention as broadly claimed at the time of filing.
Applicant’s arguments regarding rejection under 35 USC 112(a)
Applicant's arguments filed 3/17/2026 have been fully considered but they are not persuasive.
Applicant argues on pages 1-2 of the Remarks that the claims have been amended to require the modification being position 14 of SEQ ID NO: 1 and that dependent claims limit the scope to Meloidogyne incognita and to a tomato plant. Applicant argues that the instantly claimed scope is supported by the written description. Applicant refers to Example 2 which demonstrates improved resistance in tobacco and Arabidopsis. Applicant argues that Example 1 determined that the first 108 amino acids of the SmD1 protein interact with the nematode effector, highlighting this domain as a target. Applicant argues that because position 14 is within the first 108 positions, one would expect the same phenotype with other SmD1 proteins with at least 90% identity to SEQ ID NO: 1.
This argument has been fully considered but it is not persuasive. It is not clear that all sequences sharing as little as 90% identity to SEQ ID NO: 1 comprise an SmD1. It is not clear that all of the sequences within this genus, if mutated at position 14, would confer nematode resistance in any plant to any species of nematode within genus Meloidogyne. While Applicant has described improvement of resistance to the nematode of species Meloidogyne incognita in a tomato, Arabidopsis and Nicotiana benthamiana by disrupting the plant’s SmD1 gene within the SmD1 domain, Applicant has not described a structure that would provide this function across any nematode nor any nematode species within the genus Meloidogyne. Williamson (Williamson and Hussey. The Plant Cell. 8: 1735-1745. 1996) teaches that different nematode species, including different species within the genus Meloidogyne, affect different species of plants and do not share resistance loci (Table 1). Williams teaches that Solanum plants tomato and potato have different pathogenic nematode species (Table 1). The observation that the SmD1 domain is conserved across plants does not satisfy the lack of working examples or description of a structure that would allow one to envision which members of the claimed genus comprise nematode resistance given the variability of nematode pathogenicity in the prior art.
Closest prior art
Claims 1, 4-12, 14-16 and 19-21 are free of the prior art. The closest prior art is Klepadlo (Klepadlo et al. 2018. Crop Science. 58:2511-2522). Klepadlo teaches that mapping resistance to soybean root-knot nematode as reported genomic regions including the Rmi1 gene. Klepadlo teaches many soybean root-knot nematode resistant cultivars carry this gene (paragraph bridging pages 2512-2513). Klepadlo teaches identifying potential sources of resistance across multiple genera and races of nematodes (Table 2). Klepadlo does not teach or suggest a modified SmD1 protein comprising a missense mutation conferring improved nematode resistance. Additionally, Poraty-Gavra (US 9,834,782) discloses a protein, SEQ ID NO: 7173 (Table 2), which is similar to the instantly claimed SmD1 protein; however, Poraty-Gavra does not teach or suggest modifying the protein with a missense mutation or selecting for a modified version of the protein comprising a missense mutation to confer improved nematode resistance in a plant.
Alignment of instant SEQ ID NO: 2 to SEQ ID NO: 7173 of US 9,834,782:
Query Match 99.0%; Score 579; DB 1; Length 114;
Best Local Similarity 99.1%;
Matches 113; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MKLVRFLMKLNNEIVSIELKNGTVVHGTITGVDVSMNTHLKAVKITLKGKNPVTLDHLSV 60
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKLVRFLMKLNNESVSIELKNGTVVHGTITGVDVSMNTHLKAVKITLKGKNPVTLDHLSV 60
Qy 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGKPMGRGRGRGRGRGRGRGR 114
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGKPMGRGRGRGRGRGRGRGR 114
Alignment of instant SEQ ID NO: 1 to SEQ ID NO: 7129 of WO2013179211:
Query Match 97.8%; Score 573; Length 114;
Best Local Similarity 94.7%;
Matches 108; Conservative 5; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MKLVRFLMKLNNETVSIELKNGTVVHGTITGVDVSMNTHLKAVKITLKGKNPVTLDHLSV 60
|||||||||||||||||||||||:|||||||||:||||||| ||:|||||||||:|||||
Db 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVTMDHLSV 60
Qy 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGKPMGRGRGRGRGRGRGRGR 114
|||||||||||||||||||||||||||||||||||||:||||||||||||||||
Db 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGKPLGRGRGRGRGRGRGRGR 114
Conclusion
Claims 1, 4-12, 14-16 and 19-21 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID R BYRNES whose telephone number is (571)270-3935. The examiner can normally be reached 9:00 - 5:00 M-F.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/DAVID R BYRNES/ Examiner, Art Unit 1662
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