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 .
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Election/Restrictions
Applicant's election with traverse of the invention of Group 1 in the reply filed on 06/24/2026 is acknowledged. The traversal is on the grounds that examining the invention of Group 2, drawn to a process of using identified markers to identify plants comprising a modified Tom2a gene, would not involve an undue search burden when examining the invention of Group 1. This is not found persuasive. While Examiner has withdrawn the Species Election requirement with regard to the invention of Group 1 (Examiner searched all of SEQ ID Nos:1-12 in multiple databases), the original restriction has a proper and reasonable basis and the search of an additional 10 sequences in the context of an invention that does not require any of the modified Tom2a genes of Group 1 is reasonably deemed to involve undue search burden.
The requirement is still deemed proper and is therefore made FINAL.
Status of the Claims
Claims 1-48 are pending.
Claim 19 is withdrawn as being directed to a non-elected invention.
Claims 1-18, 20-48 are examined herein.
Claim Objections
Claims 8, 20 and 28 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3, 5, 7, 17-18, 22, 24, 26-28, 30, 32-33, 35, 37, 39, 41, 43 and 47 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has clarified the written description requirement. The court stated that a written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not description of that material". Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
Applicant claims mutations of Tom2a homologues that have at least 70% identity to SEQ ID NO:1 that, when modified, produce the function of increased tobamovirus resistance. In Claims 22 and 37 there are no structural limitations on the Tom2a genes. At 70% identity to SEQ ID NO:1, 252 substitutions, deletions or additions are allowed over the 840 nucleic acids of SEQ ID NO:1. This would allow for any and all of the amino acids in the encoded polypeptides to be deleted or substituted.
The genus of polypeptides that are encompassed by these structural limitations is vast. However, because the claims are directed to modification of existing genes, it is reasonable to interpret the claims as encompassing genes that are extant in nature. Nevertheless, the size of this genus is unknown, as is the genus of plants that comprise said genes. SEQ ID NO:1 is a cucumber gene and it is therefore reasonable to conclude that the genus of plants encompassed by the claims includes any number of plant species and varieties that are related to cucumber at some genetic distance.
Applicant describes specific Tom2a gene and polypeptide sequences by sequence identifiers (SEQ ID NOs 1-6 and 7-12) and select mutants thereof. Applicant describes a mutational approach coupled with TILLING to arrive at a set of mutations in the cucumber Tom2a gene that resulted in substitutions and truncations that led to CGMMV resistance. (Examples 1 and 2). Applicant describes a similar approach with tomato plants that included further efforts to generate mutants using CRISPR targeting the Tom2a gene. The results showed that in tomato the disruption of Tom2a function produced plants resistant to ToBRFV. (Examples 5-6).
The structural features that distinguish Tom2a genes or homologues thereof having the required structural identity, that function to increase a tomato plant’s resistance to any Tobamovirus, when Tom2a function is inhibited by modification are not described in the specification, nor is any direction given to be able to find Tom2a genes or homologue thereof that would confer said functions when modified in any related species due to the lack of disclosure regarding the structural features that define Tom2a genes or homologues thereof.
The state of the art for inferring a structure function relationship based on sequence homology is highly unpredictable. The functional prediction of a protein based on structural comparison is not consistent with an empirical assessment of its function. For example, Doerks et al. (TIG, 14:248-250, 1998) teaches that sequence homology is not sufficient to determine functionality of an uncharacterized protein. The homologs that scored best in PSI-BLAST analysis failed to share same catalytic activity. The reference clearly emphasizes that computer analysis of genome sequences is flawed, and overpredictions are common because the highest scoring database protein does not necessarily share the same or even similar functions (pg. 248, first paragraph; page 248, right column, second paragraph). Also, Smith et al. (Nature Biotechnology, 15:1222-1223, 1997) teaches that there are numerous cases in which proteins of very different functions are homologous (pg. 1222, last paragraph). Also, Bork et al. (TIG, 12:425-427, 1996) teaches that homology search methods are stretched and spurious hits are taken as real. The reference further teaches that similarities determined by homology search might only be restricted to certain domains of the uncharacterized protein, whereas the whole protein is required for the functionality of the protein (pg. 426, right column, first paragraph).
The Applicant does not describe the structural features of genes or homologues thereof from any cucumber-related plant species that confer the function of increasing the plant’s resistance to Tobamoviruses when the recited genes undergo a loss of function.
The effects of disrupting Tom2a function on Tobomovirus multiplication in plants is not predictable. Ishibashi, et al. "Interactions between tobamovirus replication proteins and cellular factors: their impacts on virus multiplication." Molecular plant-microbe interactions 23.11 (2010): 1413-1419 teaches that Knockout of the TOM2A gene and some of its homologs in A. thaliana partially inhibits the multiplication of a crucifer-infecting tobamovirus (Tobacco mosaic virus [TMV]-Cg) but has little effect on the multiplication of Tomato mosaic virus (ToMV; genus Tobamovirus). Thus, Ishibashi teaches, TOM2A is most likely not an essential factor of tobamovirus multiplication but functions as an enhancer of replication complex formation of some tobamoviruses. (¶ spanning p. 1413-1414). As such, predicting whether disrupting any particular homologue of Tom2a having the structural requirements of the claims would produce the effect of increasing tobomovirus resistance would require a description of the structure-function relationship of Tom2a homologues that is not found in the prior art or in the instant disclosure. The limited examples provided by Applicant, restricted to working examples in two species, is insufficient to describe the claimed genus by virtue of example.
Hence, Applicant has not, in fact, described the claimed invention within the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
Claims 13, 14 and 16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for using Tom2a genes having the sequences specifically identified in the instant disclosure, does not reasonably provide enablement for using the genes as encompassed by the range of the claims.
In re Wands, 858 F.2d 731 (Fed. Cir. 1988) lists the following eight factors for determining whether undue experimentation would be required to practice an invention: (1) quantity of experimentation necessary; (2) amount of direction or guidance supplied; (3) presence or absence of working examples; (4) nature of the invention; (5) state of the prior art; (6) relative skill of those in the art; (7) predictability or unpredictability or the prior art; (8) breadth of the claims.
Applicant claims a modified Tom2a gene encoding a Tom2a protein comprising a deletion, a substitution, or an insertion of at least one amino acid when compared to a homologous sequence having at least 70% sequence similarity to SEQ ID No. 7. The scope of polypeptides having 70% similarity to SEQ ID NO:7 includes polypeptides with 83 substitutions, deletions or additions relative to the 279 amino acid residues of SEQ ID NO:1.
Applicant teaches specific Tom2a gene and polypeptide sequences by sequence identifiers (SEQ ID NOs 1-6 and 7-12) and select mutants thereof. Applicant teaches a mutational approach coupled with TILLING to arrive at a set of mutations in the cucumber Tom2a gene that resulted in substitutions and truncations that led to CGMMV resistance. (Examples 1 and 2). Applicant teaches a similar approach with tomato plants that included further efforts to generate mutants using CRISPR targeting the Tom2a gene. The results showed that in tomato the disruption of Tom2a function produced plants resistant to ToBRFV. (Examples 5-6).
Applicant does not provide teachings sufficient to enable one of ordinary skill in the art to use the invention across the scope of the claims without undue experimentation.
The effects of disrupting Tom2a function on Tobomovirus multiplication in plants is not predictable. Ishibashi, et al. "Interactions between tobamovirus replication proteins and cellular factors: their impacts on virus multiplication." Molecular plant-microbe interactions 23.11 (2010): 1413-1419 teaches that Knockout of the TOM2A gene and some of its homologs in A. thaliana partially inhibits the multiplication of a crucifer-infecting tobamovirus (Tobacco mosaic virus [TMV]-Cg) but has little effect on the multiplication of Tomato mosaic virus (ToMV; genus Tobamovirus). Thus, Ishibashi teaches, TOM2A is most likely not an essential factor of tobamovirus multiplication but functions as an enhancer of replication complex formation of some tobamoviruses. (¶ spanning p. 1413-1414). As such, predicting whether disrupting any particular homologue of Tom2a having the structural requirements of the claims would produce the effect of increasing tobomovirus resistance would require a description of the structure-function relationship of Tom2a homologues that is not found in the prior art or in the instant disclosure. The working examples provided by Applicant do not enable the use of the range of mutant Tom2a genes as encompassed by the claims.
Given the limited guidance supplied by Applicant, the breadth of the claims and the nature of the invention, as well as the unpredictability in the art, it would have required one skilled in the art undue trial and error experimentation to practice the claimed invention through the full scope of its claims.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 16 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 16 recites “Seed of or from the plant of claim 1, or comprising a modified Tom2a gene that leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification.”
Claim 16 recites both dependency from Claim 1, or limitations that are independent of Claim 1. This claim is not in proper dependent form pursuant to the plain language of 35 U.S.C. 112(d). For purposes of examination, the claim is interpreted to read in part “Seed of or from the plant of claim 1, comprising a modified Tom2a gene…”. This interpretation does not relieve Applicant of the duty to amend the claim to address the cited deficiency.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-7, 9-18, 22-25, 31-35, 37, 39, 42 and 44-48 rejected under 35 U.S.C. 102(A)(1) as being anticipated by Hu, Qun, et al. "Two TOBAMOVIRUS MULTIPLICATION 2A homologs in tobacco control asymptomatic response to tobacco mosaic virus." Plant Physiology 187.4 (2021): 2674-2690, taken with evidence of the instant Specification.
Applicant claims a plant comprising a modified Tom2a gene, the wildtype of which comprises SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, or SEQ ID No. 6, or comprises another homologous sequence having at least 70% sequence identity to SEQ ID No. 1, which modified gene leads to increased resistance to a Tobamovirus (Claim 1), the plant of claim 1, which comprises a modification in the Tom2a gene that leads to a modified Tom2a protein that has a deletion, a substitution, or an insertion of at least one amino acid when compared to SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, or SEQ ID No. 12, or compared to another homologous sequence having at least 70% sequence similarity to SEQ ID No. 7 (Claim 2), the plant of claim 1, wherein the modification results in a premature stop codon which leads to a truncated protein, or wherein the Tom2a protein encoded by the modified Tom2a gene is absent, has a changed function, a reduced function, or is non- functional (Claim 3), the plant of claim 1, wherein the modification in the Tom2a protein is present in a transmembrane domain or in the C-terminal tail, or wherein the modification in the Tom2a protein is present in Non-CP EC1 or Non-CP EC2 (Claim 5), the plant of claim 1, wherein the modified Tom2a protein is truncated and comprises only amino acids 1-267 of SEQ ID No. 7 or less, or the corresponding number of amino acids of a homologous Tom2a protein sequence, or the modified Tom2a protein comprises a modification in amino acids 268-279 of SEQ ID No. 7 that leads to a changed function, a reduced function, or a non-functional protein, or in the corresponding amino acids of a homologous Tom2a protein sequence having the sequence of SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, or SEQ ID No. 12 (Claim 7), the plant of claim 1, which is a Cucurbitaceae or Solanaceae plant (Claim 9), the plant of claim 9, which is a Cucumis sativus plant, Cucumis melo plant, Citrullus lanatus plant, Cucurbita pepo plant, Solanum lycopersicum plant, or Capsicum annuum plant (Claim 10), the plant of claim 9 or 10, which is a Cucurbitaceae plant having increased resistance to Cucumber Green Mottle Mosaic Virus (CGMMV) or a Solanacae plant having increased resistance to Tomato Brown Rugose Fruit Virus (ToBRFV) (Claim 11), seed of or from the plant of claim 1, comprising (see 112d rejection) a modified Tom2a gene that leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification (Claim 18), Propagation material suitable from or for producing the plant of claim 1, wherein the propagation material is suitable for sexual reproduction, and comprises a microspore, pollen, an ovary, an ovule, an embryo sac, or an egg cell; or the propagation material is suitable for vegetative reproduction and comprises a cutting, a root, a stem cell, or-a protoplast; or the propagation material is suitable for tissue culture of regenerable cells and comprises a leaf, pollen, an embryo, a cotyledon, a hypocotyl, a meristematic cell, a root, a root tip, an anther, a flower, a seed, and or a stem; wherein the plant produced from the propagation material comprises the modified Tom2a gene that provides increased resistance to a Tobamovirus, and that leads to a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification (Claim 32), a method for producing seed comprising growing a plant from the seed of claim 18, allowing the plant to produce a fruit with seed, harvesting the fruit, and extracting seed from the fruit (Claim 33), the plant of claim 10, which is a Cucumis sativus plant or Solanum lycopersicum plant (Claim 34), a Cucurbitaceae-plant having CGMMV resistance, or a Solanaceae plant and the having ToBRFV produced from the propagation material of claim 32 (Claim 47).
Applicant further claims a Cucurbitaceae or Solanaceae plant comprising a modified Tom2a gene, wherein the Cucurbitaceae plant has resistance to Cucumber Green Mottle Mosaic Virus (CGMMV) and the Solanacae plant has resistance to Tomato Brown Rugose Fruit Virus (ToBRFV), and the modified Tom2a gene leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification, wherein: the wildtype Tom2a Tom2a gene has a sequence which comprises SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, or a homologous sequence having at least 95% sequence identity to SEQ ID No. 1, andthe wildtype Tom2a protein has a sequence which comprises SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, or a sequence having at least 95% sequence similarity to SEQ ID No. 7 (Claim 4), the plant of claim 4, which is a Cucumis sativus plant, Cucumis melo plant, Citrullus lanatus plant, Cucurbita pepo plant, Solanum lycopersicum plant, or Capsicum annuum plant (Claim 6), Seed of, or that produces, the plant of claim 4 (Claim 12), propagation material suitable from or for producing the plant of claim 4, wherein the propagation material is suitable for sexual reproduction, and comprises a microspore, pollen, an ovary, an ovule, an embryo sac, or an egg cell; or the propagation material is suitable for vegetative reproduction and comprises a cutting, a root, a stem cell, or-a protoplast; or the propagation material is suitable for tissue culture of regenerable cells and comprises a leaf, pollen, an embryo, a cotyledon, a hypocotyl, a meristematic cell, a root, a root tip, an anther, a flower, a seed, or a stem; wherein the plant produced from the propagation material comprises the modified Tom2a gene (Claim 15), Seed of claim 12, wherein the plant is a Cucumis sativus plant,Cucumis melo plant, Citrullus lanatus plant, Cucurbita pepo plant, Solanum lycopersicum plant, or Capsicum annuum plant (Claim 23), propagation material of claim 15, wherein the plant is a Cucumis sativus plant,Cucumis melo plant, Citrullus lanatus plant,Cucurbita pepo plant, Solanum lycopersicum plant, or Capsicum annuum plant (Claim 25), the plant of claim 4, which is a Cucumis sativus plant or a Solanum lycopersicum plant (Claim 42), seed of claim 12 which is Cucumis sativus seed or Solanum lycopersicum seed (Claim 44), propagation material of claim 15, wherein the plant is Cucumis sativus plant or Solanum lycopersicum plant (Claim 48).
Applicant further claims a modified Tom2a gene encoding a Tom2a protein comprising a deletion, a substitution, or an insertion of at least one amino acid when compared to SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, or SEQ ID No. 12, or compared to another homologous sequence having at least 70% sequence similarity to SEQ ID No. 7 (Claim 13), the modified Tom2a gene of claim 13, which modified gene comprises a premature stop codon and which encodes a truncated Tom2a protein, or wherein the Tom2a protein encoded by the modified Tom2a gene is absent, has a changed function, a reduced function, or is non-functional (Claim 14), the modified Tom2a gene of claim 13, wherein the encoded modified Tom2a protein is truncated and comprises only amino acids 1-267 of SEQ ID No. 7 or less, or the corresponding number of amino acids of a homologous Tom2a protein sequence, or the modified Tom2a protein comprises a modification in amino acids 268-279 of SEQ ID No. 7 that leads to a changed function, a reduced function, or a non-functional protein, or in the corresponding amino acids of a homologous Tom2a protein sequence having the sequence of ef SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, or SEQ ID No. 12 (Claim 16), the modified Tom2a gene of claim 13, wherein the presence of the modified gene in a plant leads to increased Tobamovirus resistance (Claim 17), the modified Tom2a gene of claim 17, wherein the plant is a Cucurbitaceae plant and the Tobamovirus is CGMMV, or the plant is a Solanaceae plant and the Tobamovirus is ToBRFV (Claim 35).
Applicant further claims a method for increasing Tobamovirus resistance in a plant comprising introducing a modification in a Tom2a gene and thereby producing in the plant a modified Tom2a gene, or comprising introducing into the plant a modified Tom2a gene, wherein the modified Tom2a gene leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification (Claim 22), the method of claim 22, wherein the Tobamovirus is CGMMV or ToBRFV (Claim 37).
Applicant further claims a method for producing a Cucurbitaceae or Solanaceae plant that has increased Tobamovirus resistance comprising introducing a modification in a Tom2a gene comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, or SEQ ID No. 6, or in another homologous sequence having at least 70% sequence identity to SEQ ID No. 1, wherein the modified Tom2a gene leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification (Claim 24), The method of claim 24, wherein the plant is a Cucurbitaceae plant and the Tobamovirus is CGMMV or the plant is a Solanaceae plant and the Tobamovirus is ToBRFV (Claim 39).
Applicant further claims a method for identifying a plant comprising a modified Tom2a gene that leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification, the method comprising: determining by genetic analysis modification in a Tom2a gene comprising SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, or in another Tom2a gene having at least 95% sequence identity to the sequence of SEQ ID No. 1, and optionally analyzing if the plant comprising the modification has increased resistance to a Tobamovirus (Claim 31), the method of claim 31, wherein the Tobamovirus is CGMMV or ToBRFV (Claim 45), the method of claim 45, including performing the analyzing step (Claim 46).
Hu discloses Solanum lycopersicum (tomato) plants wherein the Tom2a gene has been largely deleted (said deletion encompassing transmembrane domains) to test the effects on TMV tolerance. The deletion appears to eliminate most of the encoded polypeptide including the transmembrane domains. (p. 2678 right col. ¶ 1 – p. 2681 left col. ¶ 2, Supplemental Figure S2). The Tom2a gene in the tomato plants was modified by CRISPR gene editing techniques, producing a first transformant generation, which was analyzed for the presence of mutations and the mutations were then sequenced (Supplemental Figure S2) and the mutant plants were selfed to produce homozygous nulls in the next generation. (p. 2688 left col. ¶ 5 – right col. ¶ 2). Hu discloses that the resultant Tom2a-null homozygotes showed significantly increased tolerance to TMV. An alignment between the mRNA sequence of the Tom2a gene in tomato that was targeted for CRISPR-type deletion as disclosed by Hu, showing 100% identity is as follows:
Score
Expect
Identities
Gaps
Strand
1580 bits(855)
0.0
855/855(100%)
0/855(0%)
Plus/Plus
Query 1 ATGGCGTGCAAAGGGTTTTGGGAGTGCTTGTTGAAGCTCTTGAACTTTTTGTTGACCCTT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 226 ATGGCGTGCAAAGGGTTTTGGGAGTGCTTGTTGAAGCTCTTGAACTTTTTGTTGACCCTT 285
Query 61 GTTGGTTTGACAATGGTGGGGTATGGTATTTATCTATTTGTTGAGTACAAAAATCATTCA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 286 GTTGGTTTGACAATGGTGGGGTATGGTATTTATCTATTTGTTGAGTACAAAAATCATTCA 345
Query 121 CACTCCGGAGATGATTACCCAGTTGCACCACCTATGAGTGGTGACATGATAGAGTTTGGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 346 CACTCCGGAGATGATTACCCAGTTGCACCACCTATGAGTGGTGACATGATAGAGTTTGGT 405
Query 181 CGTCCAATGCTGATGGCTGTATCGTTGGCTGAAAACATATTTGATAAACTTCCAAAACCT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 406 CGTCCAATGCTGATGGCTGTATCGTTGGCTGAAAACATATTTGATAAACTTCCAAAACCT 465
Query 241 TGGTTCATATATTTGTTTATTGGTATTGGAGCAGTTCTTGTAGTTGTATCTTGCTGTGGT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 466 TGGTTCATATATTTGTTTATTGGTATTGGAGCAGTTCTTGTAGTTGTATCTTGCTGTGGT 525
Query 301 TGTATTGGAGCGGCAACAAGGAATGGTTGCTGCCTGAGTTGTTACTCCATGTTGATTTTC 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 526 TGTATTGGAGCGGCAACAAGGAATGGTTGCTGCCTGAGTTGTTACTCCATGTTGATTTTC 585
Query 361 TTGTTGATCTTGGTAGAGCTAGGTGCTGCTGGTTTTATATTCTTTGATAAAAGCTGGAAA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 586 TTGTTGATCTTGGTAGAGCTAGGTGCTGCTGGTTTTATATTCTTTGATAAAAGCTGGAAA 645
Query 421 GATGAAATTCCAAGGGATAAAACGGGCAACTTTGAAACGATCTATGACTTTCTGGATGAC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 646 GATGAAATTCCAAGGGATAAAACGGGCAACTTTGAAACGATCTATGACTTTCTGGATGAC 705
Query 481 CACTGGAAGATTATTAAGTGGGTTGCCCTTGGTGCTGTTATATTCGAGGCTCTTATATTC 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 706 CACTGGAAGATTATTAAGTGGGTTGCCCTTGGTGCTGTTATATTCGAGGCTCTTATATTC 765
Query 541 TTATTGGCCCTCGTAGTAAGGGCAGCAAACAGACCAGCAGACTATGATAGTGATGATGAG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 766 TTATTGGCCCTCGTAGTAAGGGCAGCAAACAGACCAGCAGACTATGATAGTGATGATGAG 825
Query 601 TACATAGGTGGTCCCAGACAACAAATCCGACAGCCACTGATCAACAATAGGCCACCAGCA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 826 TACATAGGTGGTCCCAGACAACAAATCCGACAGCCACTGATCAACAATAGGCCACCAGCA 885
Query 661 AATCCTGCAACTGGTGTCCCTGTTACTGCTACTCTTGATAATCGTCCAAGTAGAAATGAT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 886 AATCCTGCAACTGGTGTCCCTGTTACTGCTACTCTTGATAATCGTCCAAGTAGAAATGAT 945
Query 721 GCGTGGAGTACACGTATGAGGGAAAAGTATGGACTTGACACATCAGAGTTTACTTACAAC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 946 GCGTGGAGTACACGTATGAGGGAAAAGTATGGACTTGACACATCAGAGTTTACTTACAAC 1005
Query 781 CCATCGGAGTCGAACAGATATCCGCCAACTGCCGCACAGCCGCAAGAGGAAAGGAAGGGT 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1006 CCATCGGAGTCGAACAGATATCCGCCAACTGCCGCACAGCCGCAAGAGGAAAGGAAGGGT 1065
Query 841 TGTACCATAATGTGA 855
|||||||||||||||
Sbjct 1066 TGTACCATAATGTGA 1080
An alignment between the sequence encoded by the mRNA of the gene targeted by Hu, showing 100% identity with the instant SEQ ID NO:11 is as follows:
Score
Expect
Method
Identities
Positives
Gaps
590 bits(1521)
0.0
Compositional matrix adjust.
284/284(100%)
284/284(100%)
0/284(0%)
Query 1 MACKGFWECLLKLLNFLLTLVGLTMVGYGIYLFVEYKNHSHSGDDYPVAPPMSGDMIEFG 60
MACKGFWECLLKLLNFLLTLVGLTMVGYGIYLFVEYKNHSHSGDDYPVAPPMSGDMIEFG
Sbjct 1 MACKGFWECLLKLLNFLLTLVGLTMVGYGIYLFVEYKNHSHSGDDYPVAPPMSGDMIEFG 60
Query 61 RPMLMAVSLAENIFDKLPKPWFIYLFIGIGAVLVVVSCCGCIGAATRNGCCLSCYSMLIF 120
RPMLMAVSLAENIFDKLPKPWFIYLFIGIGAVLVVVSCCGCIGAATRNGCCLSCYSMLIF
Sbjct 61 RPMLMAVSLAENIFDKLPKPWFIYLFIGIGAVLVVVSCCGCIGAATRNGCCLSCYSMLIF 120
Query 121 LLILVELGAAGFIFFDKSWKDEIPRDKTGNFETIYDFLDDHWKIIKWVALGAVIFEALIF 180
LLILVELGAAGFIFFDKSWKDEIPRDKTGNFETIYDFLDDHWKIIKWVALGAVIFEALIF
Sbjct 121 LLILVELGAAGFIFFDKSWKDEIPRDKTGNFETIYDFLDDHWKIIKWVALGAVIFEALIF 180
Query 181 LLALVVRAANRPADYDSDDEYIGGPRQQIRQPLINNRPPANPATGVPVTATLDNRPSRND 240
LLALVVRAANRPADYDSDDEYIGGPRQQIRQPLINNRPPANPATGVPVTATLDNRPSRND
Sbjct 181 LLALVVRAANRPADYDSDDEYIGGPRQQIRQPLINNRPPANPATGVPVTATLDNRPSRND 240
Query 241 AWSTRMREKYGLDTSEFTYNPSESNRYPPTAAQPQEERKGCTIM 284
AWSTRMREKYGLDTSEFTYNPSESNRYPPTAAQPQEERKGCTIM
Sbjct 241 AWSTRMREKYGLDTSEFTYNPSESNRYPPTAAQPQEERKGCTIM 284
Seeds of the mutant tomato plants of Hu, plant parts and propagation materials derived from said plant (tissues, gametes) and progeny thereof are deemed to be inherent as inherently occurring parts or products of said plants. Applicant’s specification provides evidence that knockouts of Tom2a, including substitutions, truncations and deletions, confer tolerance to ToBRFV. (See Examples 4-6). As such, and without evidence to the contrary, it is reasonable to conclude that tolerance of ToBRFV is an inherent quality of the mutant tomato plants of Hu.
The claims are therefore anticipated by the disclosures of the prior art.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 21, 26-30, 36, 40-41 and 43 are rejected under 35 U.S.C. 103 as being unpatentable over Hu, Qun, et al. "Two TOBAMOVIRUS MULTIPLICATION 2A homologs in tobacco control asymptomatic response to tobacco mosaic virus." Plant Physiology 187.4 (2021): 2674-2690 in view of Vijeth, S., et al. "Evaluation of tomato hybrids for resistance to leaf curl virus disease and for high-yield production." Horticulture, Environment, and Biotechnology 59.5 (2018): 699-709, taken with evidence of the instant Specification.
Applicant claims a plant comprising a modified Tom2a gene, the wildtype of which comprises SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, or SEQ ID No. 6, or comprises another homologous sequence having at least 70% sequence identity to SEQ ID No. 1, which modified gene leads to increased resistance to a Tobamovirus (Claim 1), a method for the production of a plant which has increased resistance to a Tobamovirus comprising: a) crossing the plant of claim 1, with another plant; b) optionally performing one or more rounds of selfing and/or crossing of the plant resulting from the cross of step a) to obtain a further generation population; c) selecting from the population resulting from the cross of step a), or from the further generation population of step b), a plant that comprises the modified Tom2a gene or exhibits Tobamovirus resistance (Claim 26), a method for producing a hybrid seed, comprising crossing a first parent plant with a second parent plant and harvesting the resultant hybrid seed, wherein the first parent plant and/or the second parent plant is the plant of claim 1, and wherein the hybrid plant that is grown from the seed has the modified Tom2a Tom2a gene and increased Tobamovirus resistance (Claim 27), the method of claim 27, wherein the hybrid seed is Cucumis sativus seed having increased CGMMV resistance, or the hybrid seed is Solanum lycopersicum seed having increased ToBRFV resistance (Claim 28), the hybrid seed produced by the method of claim 27 (Claim 30), the method of claim 27, wherein the hybrid plant that is grown from the seed is a Cucurbitaceae-plant and the Tobamovirus is CGMMV or the plant is a Solanaceae plant and the Tobamovirus is ToBRFV (Claim 43),
Applicant further claims a Cucurbitaceae or Solanaceae plant comprising a modified Tom2a gene, wherein the Cucurbitaceae plant has resistance to Cucumber Green Mottle Mosaic Virus (CGMMV) and the Solanacae plant has resistance to Tomato Brown Rugose Fruit Virus (ToBRFV), and the modified Tom2a gene leads to: a transmembrane domain modified Tom2a protein, or a C-terminal tail truncated Tom2a protein, or a Tom2a protein having modification in the Non-CP EC1 loop, or a Tom2a protein having the Non-CP EC2 loop, or a Tom2a protein consisting of amino acids 1-267 of SEQ ID No. 7 or corresponding amino acids of a homologous Tom2a protein sequence, or a Tom2a protein having a modification in amino acids 268-279 of SEQ ID No. 7 or corresponding amino acids in a homologous Tom2a protein sequence, or an absence of Tom2a protein, or an absence of Tom2a protein function, or a Tom2a protein having reduced function in comparison with Tom2a protein function from a Tom2a gene not having the modification, wherein: the wildtype Tom2a Tom2a gene has a sequence which comprises SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, or a homologous sequence having at least 95% sequence identity to SEQ ID No. 1, andthe wildtype Tom2a protein has a sequence which comprises SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, or a sequence having at least 95% sequence similarity to SEQ ID No. 7 (Claim 4), a method for producing a Solanacae plant having ToBRFV resistance comprising:a) crossing the Solanacae plant of claim 4 with another Solanacae plant;b) optionally performing one or more rounds of selfing and/or crossing of the Solanacae plant resulting from the cross of step a) to obtain a further generation population; c) selecting from the population resulting from the cross of step a), or from the further generation population of step b), a Solanacae plant that comprises the modified Tom2a gene or exhibits ToBRFV resistance (Claim 21), a method for producing a hybrid Cucurbitaceae plant seed or hybrid Solanacae plant, comprising crossing a first Cucurbitaceae parent plant with a second Cucurbitaceae parent plant or crossing a first Solanacae parent plant with a second Solanacae parent plant and harvesting the resultant hybrid seed, wherein the first parent plant and/or the second parent plant is the Cucurbitaceae plant or the Solanacae plant of claim 4, and wherein the Cucurbitaceae hybrid plant grown from the seed has CGMMV resistance and the Solanacae hybrid plant grown from the seed has ToBRFV resistance (Claim 29), the method of claim 29, wherein the Cucurbitaceae plant is a Cucumis sativus plant,Cucumis melo plant, Citrullus lanatus plant, or Cucurbita pepo plant, and the Solanacae plant is Solanum lycopersicum plant or Capsicum annuum plant (Claim 36), the method of claim 21, wherein the Solanacae plant is Solanum lycopersicum plant or Capsicum annuum plant (Claim 40).
Hu taches Solanum lycopersicum (tomato) plants wherein the Tom2a gene has been largely deleted (said deletion encompassing transmembrane domains) to test the effects on TMV tolerance. The deletion appears to eliminate most of the encoded polypeptide including the transmembrane domains. (p. 2678 right col. ¶ 1 – p. 2681 left col. ¶ 2, Supplemental Figure S2). The Tom2a gene in the tomato plants was modified by CRISPR gene editing techniques, producing a first transformant generation, which was analyzed for the presence of mutations and the mutations were then sequenced (Supplemental Figure S2) and the mutant plants were selfed to produce homozygous nulls in the next generation. (p. 2688 left col. ¶ 5 – right col. ¶ 2). Hu teaches that the resultant Tom2a-null homozygotes showed significantly increased tolerance to TMV. Alignments showing 100% identity between the mutated genes of Hu and the instant SEQ ID Nos:6 and 11 at the nucleic acid and amino acid residue level are set forth previously herein.
However, Hu does not teach that the mutant plants comprising null Tom2a genes were crossed to another plant to produce progeny such as hybrid progeny.
Vijeth teaches crossing parental lines comprising Ty-1, Ty-2 and Ty-3 ToLCV resistance alleles to various other lines, and then testing the resultant hybrids for tolerance to the virus and other agronomic traits. Vijeth teaches that about half of the hybrids exhibited ToLCV resistance. (p. 700 left col. ¶ 2, p. 704 right col. ¶ 2). Vijeth teaches a correlation analysis among the hybrids revealed that breeding for ToLCV-resistant hybrids significantly improved total yield, fruit weight and lycopene content of the fruits. (p. 708 left col. ¶ 3).
It would have been prima facie obvious to a person of ordinary skill in the art at the time of filing to modify the process of Hu such that the Tom2a TMV resistance allele-comprising tomato plants are then crossed to create hybrids that are tested for disease tolerance and other agronomic traits. One having ordinary skill in the art would have been motivated to do this because Vijeth teaches that breeding for virus-resistant hybrids significantly improved total yield, fruit weight and lycopene content of the fruits.
As such, the claimed inventions are obvious in view of the teachings of the prior art.
Conclusion
No claims are allowed.
Claims 8, 20 and 38 appear to be free of the prior art. The closest prior art is Hu, Qun, et al. "Two TOBAMOVIRUS MULTIPLICATION 2A homologs in tobacco control asymptomatic response to tobacco mosaic virus." Plant Physiology 187.4 (2021): 2674-2690, the disclosures and teachings of which are set forth previously herein. However, Hu does not disclose the Tom2a gene of a Cucurbitaceae plant and the sequences of the Cucurbitaceae plants as they appear in the instant disclosure do not appear to be explicitly taught in the prior art as a reasonable target for mutation. Further, a modified Tom2a gene that comprises SEQ ID NO:14 would require a mutation in the C-terminal-most part of the gene and such a mutation does not appear to be obvious in view of the teachings of the prior art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHARLES A LOGSDON whose telephone number is (571)270-0282. The examiner can normally be reached M-F 8:30 - 5:00 pm.
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/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
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