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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 3/23/2026 has been entered.
Claim Status
Claims 1-14 are pending and being examined.
All previous objections and rejections not set forth below have been withdrawn in view of applicant’s amendments to the claims.
Claim Rejections - 35 USC § 112(a)
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.
Scope of Enablement
Claims 1-10 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 detection of the DNA sequence consisting of SEQ ID NO: 2 and/or the polypeptide consisting of SEQ ID NO: 3 (encoded by the said DNA sequence), does not reasonably provide enablement for the detection based on at least one marker and/or polymorphism or single nucleotide polymorphism that are not within the coding region of the gene conferring resistance or tolerance to Cercospora. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Claim 1 recites, “… (iii) detection of at least one marker locus in the nucleotide sequence…”. Claims 3-4 depend from claim 1 and recite, “… at least one polymorphism or single nucleotide polymorphism” (SNP). Claims 6 and 9-10 also depend from claim 1 and are drawn to a method involving the use of at least two oligonucleotides including the ones being used as PCR primers.
Claim 1 is drawn to a method involving the DNA sequence comprising SEQ ID NO: 2 and/or the polypeptide encoded by SEQ ID NO: 2. The Applicant describes only one amino acid sequence, SEQ ID NO: 3, conferring resistance or tolerance to Cercospora and encoded by the cDNA sequence set forth in SEQ ID NO: 2. (spec, p. 85). The description of the invention discloses many polymorphisms present within the “resistance-conferring” SEQ ID NO: 3 that are not in the present in the “sensitive” version of the protein, i.e., SEQ ID NO: 6 (spec; page 39, last para; page 85, para 8; Fig. 1).
The Applicant describes a “marker” as “molecular markers and/or diagnostic markers” (spec, page 15, para 51-52) and proving examples of “the structural features of the markers” in Table 1B (spec, page 15, para 48, line 8-9). All markers are oligonucleotides flanking the single specific genomic location of the Cercospora resistant (or susceptible) allele. None of the markers, as provided in the example in Table 1B, can identify a plant that is resistant or tolerant to Cercospora.
However, the Applicant does not provide any guidance to identify which of the polymorphism(s) confer(s) Cercospora-resistance as present in SEQ ID NO: 3 in comparison to Cercospora-susceptible version set forth in SEQ ID NO: 6.
Current status of the art also does not describe how a skilled artisan can detect a Cercospora-resistance plant based on at least one marker polymorphism or single nucleotide polymorphism. There can be myriad variations and combinations of so many polymorphisms/ SNPs between SEQ ID NO: 3 and SEQ ID NO: 6, as shown in instant Fig. 1. The prior art does not tech how to design any oligonucleotide (PCR primers) to identify Cercospora-resistant plant without understanding which polymorphism(s), including SNP(s), confer Cercospora-resistance. It is also noted that detection of any specific target sequence by using PCR does not necessarily require that the primer(s) and the target sequence have 100% sequence identity, which depend significantly on the PCR conditions used as well.
Undue trial and error experimentations would be needed to find out which exact polymorphism including SNP(s) actually confer(s) Cercospora-resistance trait.
Based on breadth of the claims, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Claims 1- 14 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 a plant of the genus Beta, does not reasonably provide enablement for any other plant including the plants of the genus Spinacia. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Claims 1 is drawn to a method involving any plant and any Cercospora spp., while claim 8 and 11 recite “… a plant of the genus Beta or a plant of the genus Spinacia”. The Applicant describes the cDNA sequence comprising SEQ ID NO: 2 encoding the polypeptide comprising SEQ ID NO: 3 conferring resistance to a specific species of Cercospora, i.e., Cercospora beticola (page 1, para 1, line 3; page 4, last para, line 2-6), as discussed above. SEQ ID NOs: 2-3 are obtained from Beta vulgaris (Spec, page 85, para 4-5). The Applicant describes transforming Beta vulgaris to express the protein comprising SEQ ID NO: 3 (spec, page 92, example 2; page 98, example 3).
It is known in the art that there are around 659 Cercospora species (Borges et al. Six lineages of Cercospora are responsible for Cercospora leaf blight and purple seed stain on soybean in Brazil, 2025, Journal of Plant Pathology, 107:1435–1449; page 1435, para 1, line 9-10) and each species can have many strains. It is well documented that the development of resistant cultivars against Cercospora species is confronted by pathogen variability in the pathosystem against disease-causing species of Cercospora (Borges et al., page 1446, right column, para 1, line 3-5). Resistance conferred by a specific gene in a host plant is restricted against a specific Cercospora species and/or strain. Thus, a gene resulting in resistance or tolerance to a specific Cercospora species and/or strain affecting a specific plant species may not be effective to provide resistance or tolerance to a different Cercospora species and/or strain affecting different plant species.
The Applicant does not provide any guidance if and/or how expressing a polynucleotide encoding instant SEQ ID NO: 3 would confer Cercospora resistance against all known species of Cercospora in sugar beet and/or in a plant other than sugar beet.
Current status of the art does not provide any guidance to understand if and/or how expressing a polynucleotide encoding instant SEQ ID NO: 3 would confer Cercospora resistance against all Cercospora spp. and/or in all plants including spinach, other than the ones belonging to the genus Beta.
Undue trial and error experimentations would be needed to identify if and/or how expressing a polynucleotide encoding instant SEQ ID NO: 3 would confer Cercospora resistance (against any specific Cercospora spp. and/or strain) in a plant other than sugar beet.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Enablement
Claim 7 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 enablement requirement. The claim contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 7 is drawn, indirectly, to the method of claim 1 further restricting by using two primers in a PCR reaction which can hybridize to a genomic interval flanked by the markers s4p1395s01 and s4p0421s01.
The marker s4p1395s01 comprises not just one oligonucleotide/marker but three markers/oligos comprising different sequences- SEQ ID NO: 100, SEQ ID NO: 101 and SEQ ID NO: 102, which can hybridize anywhere in the genome at position from 55,312395 to 56,35582927 (sepc, p. 42, Table 1B). Similarly, the marker s4p0421s01 comprises not just one oligonucleotide/marker but three markers/oligos comprising different sequences- SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 222, which hybridize in the genome at position from 57,873,805 to 65,86730118. Thus, using one of the 3 oligonucleotide primers referred as “marker s4p1395s01” and another one of the 3 oligonucleotide primers referred as “marker s4p0421s01” would detect presence of the significantly identical (not necessarily having 100% sequence identity- based on the PCR conditions used) DNA sequences that flank both the resistant (SEQ ID NO: 2 encoding the polypeptide of SEQ ID NO: 3) and the susceptible (SEQ ID NO: 5 encoding the polypeptide of SEQ ID NO: 6) alleles.
SEQ ID NO: 3 and SEQ ID NO: 6 are allelic variants (spec, page 68, para 3) implying that the two alleles/genes are in the same chromosol location in the genome. It is not possible for a skilled artisan to identify the Cercospora resistant plant by detecting the difference between Cercospora-resistance allele (SEQ ID NO: 2) encoding the polypeptide SEQ ID NO: 3 and the Cercospora-susceptible allele (SEQ ID NO: 5) encoding the polypeptide comprising SEQ ID NO: 6 by using either the markers s4p1395s01 and s4p0421s01.
Based on breadth of the claims, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Written Description
Claims 1-10 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 claims contain 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 inventors, at the time the application was filed, had possession of the claimed invention.
Claim 1 recites, “… (iii) detection of at least one marker locus in the nucleotide sequence…”. Claims 3-4 depend from claim 1 and recite, “… at least one polymorphism or single nucleotide polymorphism” (SNP). Claims 6 and 9-10 also depends from claim 1 and is drawn to a method involving the use of at least two oligonucleotides being used as PCR primers.
Claim 1 is drawn to a method involving the DNA sequence comprising SEQ ID NO: 2 and/or the polypeptide encoded by SEQ ID NO: 2. The Applicant describes only one amino acid sequence, SEQ ID NO: 3, conferring resistance or tolerance to Cercospora and encoded by the cDNA sequence set forth in SEQ ID NO: 2. (spec, p. 85). The description of the invention discloses many polymorphisms present within the “resistance-conferring” SEQ ID NO: 3 that are not in the present in the “sensitive” version of the protein, i.e., SEQ ID NO: 6 (spec; page 39, last para; page 85, para 8; Fig. 1).
The Applicant describes a “marker” as “molecular markers and/or diagnostic markers” (spec, page 15, para 51-52) and proving examples of “the structural features of the markers” in Table 1B (spec, page 15, para 48, line 8-9). All markers are oligonucleotides flanking the single specific genomic location of the Cercospora resistant (or susceptible) allele. None of the markers, as provided in the example in Table 1B, can identify a plant that is resistant or tolerant to Cercospora.
However, the Applicant does not provide the structure function relationship to identify which of markers and/or which the polymorphism(s) confer(s) Cercospora-resistance and as present in SEQ ID NO: 3 in comparison to Cercospora-susceptible version set forth in SEQ ID NO: 6.
It is known in the art that there are around 659 Cercospora species (Borges et al., page 1435, para 1, line 9-10) and each species can have many strains. It is well documented that the development of resistant cultivars against Cercospora species is confronted by pathogen variability in the pathosystem against disease-causing species of Cercospora (Borges et al., page 1446, right column, para 1, line 3-5). Resistance conferred by a specific gene in a host plant is restricted to a specific Cercospora species and/or strain.
Current status of the art also does not describe any structure function relationship to enable a skilled artisan can detect a Cercospora-resistance plant based on at least one polymorphism or single nucleotide polymorphism in SEQ ID NO: 6 vs SEQ ID NO: 3. There can be myriad variations and combinations of so many polymorphisms/SNPs between SEQ ID NO: 3 and SEQ ID NO: 6, as shown in instant Fig. 1, possible. It would not be much possible for a skilled artisan to design any oligonucleotide (PCR primers) to identify Cercospora-resistant plant without understanding which polymorphism(s) including SNP(s) confer Cercospora-resistance. It is also noted that detection of any specific target sequence by using PCR does not necessarily require that the primer(s) and the target sequence have 100% sequence identity, which depend significantly on the PCR conditions used as well.
Considering the breadth of the claims, lack of structure function relationship of the broad genus claimed, and unpredictability of the art, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Claim Rejections - 35 USC § 112(d)
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 2 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 2 depends from claim 1 which recites “…. identifying a plant that is resistant or tolerant to Cercospora…” Claim 2 does not further restrict claim 1.
Applicant may cancel the claim, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 4 and 6 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 4 recites the limitations "the cosegregating region" in lines 12 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 4 depends from claim 1. Claim 1 is amended by removing the part reciting “cosegregating region”.
It is suggested to amend claim 4 in view of amendment in claim 1.
Claim 6 recites the limitation "the use of at least two oligonucleotides" in line 1. There is insufficient antecedent basis for this limitation in the claim. Neither claim 6 nor claim 1 mention how the at least two oligonucleotides are being used.
Claim 6 depends from claim 1 and claim 1 does not recite any “at least two oligonucleotides”.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-2 and 5-8 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 11-12 of U.S. Patent No. US 10767191B1 to Törjék et al., in view of Singh et al. (Primer Premier: Program for Design of Degenerate Primers from a Protein Sequence, 1998, BioTechniques 24:318-319).
Claim 1 of Törjék et al. (US patent 10767191B1) recites, “… a sugar beet plant comprising a nucleic acid molecule encoding a polypeptide that is able to confer resistance to Cercospora beticola in a sugar beet plant in which the polypeptide is expressed, wherein the polypeptide comprises an amino acid sequence that is at least 95% identical to the amino acid sequence according to SEQ ID NO: 3…”. SEQ ID NO: 3 of ‘719B and instant SEQ ID NO: 3 has 100% sequence identity, as discussed in the previous Office action dated 5/30/2025 (page 21-22). Sugar beet is a known commercially important plant belonging to genus Beta, as recited in instant claim 8.
The claims of Torjek et al. do not explicitly recite a method of identifying a plant having a polynucleotide comprising at least 95% sequence identity to instant SEQ ID NO: 2 conferring resistance/tolerance to Cercospora.
Singh et al. teaches a technique to use degenerate primers comprising at least two oligonucleotides, as recited in instant claims 6-7, designed from a known protein sequence for successful detection (as recited in instant claim 5) of any DNA sequence encoding the protein (page 319, last 2 para). Extraction of DNA from plant tissue(s), as recited in claim 5, is well known standard method in the art. Before the effective filing date of the invention, detecting presence or absence of a nucleotide sequence encoding a known protein using degenerate primers for PCR became well known in the art, as taught by Singh et al.
Before the effective filing date of the invention, it would have been obvious and within the scope of one of ordinary skill in the art to detect for the presence or absence of SEQ ID NO: 3 in a sugar beet plant, given that claims 1 and 12 of Torjek et al. teach that SEQ ID NO: 3 confers resistance to Cercospora beticola. It would also have been obvious to detect for the presence or absence of the gene encoding SEQ ID NO: 3 in the plant, following well-known PCR methodologies such as that taught by Singh et al. That would have been led to endogenous genomic DNA sequence comprising SEQ ID NO: 2 and/or allele(s), which is/are the functional equivalent(s) of the polypeptide comprising of SEQ ID NO: 3 and flanked by markers s4p1395s01 and s4p0421s01 (as recited in claim 7). These markers are inherently present in the endogenous gene. See the instant specification, Table 1B and the paragraph bridging p. 45-46 which teaches that these markers flank the genomic region which comprises the resistance gene. It’s crucial to note that it is the polypeptide, and not the polynucleotide encoding it, that confers Cercospora resistance. The polynucleotide sequences encoding the polypeptide consisting of SEQ ID NO: 3 are considered functional equivalents. Using and/or detecting any specific polynucleotide encoding a polypeptide consisting of SEQ ID NO: 3 is an experimental design choice of an ordinarily skilled artisan.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to identify a plant that is resistant/tolerant to Cercospora by detecting the presence or absence of a nucleotide sequence that encodes a polypeptide consisting of SEQ ID NO: 3 which is a functional equivalent of the DNA sequence having at least 95% identical to SEQ ID NO: 2 conferring resistance/tolerance to Cercospora.
Claims 9-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 11-12 of U.S. Patent No. 10767191B1 to Törjék et al., in view of Singh et al. as applied to claims 1-2 and 5-8 above, and further in view of Manley et al. (US 2014/0212877 A1).
Instant claim 9 depends from claim 1 and recites a method comprising a PCR step involving two allele-specific forward primers and wherein the detection step involves fluorescence resonant energy transfer and wherein the presence, absence or kind of the fluorescence is determined by a sensor. Instant claim 10 depends from claim 9 and requires the involvement of one common reverse primer.
Claims 1 and 11-12 of Törjék et al. in view of Singh et al. describe a method of identifying a Cercospora resistance beet plant using PCT comprising forward and reverse primers to detect a polynucleotide comprising the SEQ ID NO: 3 or any functional equivalent of the DNA sequence having at least 95% identical to SEQ ID NO: 3 conferring resistance/ tolerance to Cercospora, as discussed above.
However, the claims 1 and 11-12 of Torjek et al. in view of Sing et al., do not describe fluorescent resonance energy transfer (FRET) based method and wherein the presence, absence or kind of the fluorescence is determined by a sensor.
Manley et al. describes the method of using fluorescent resonance energy transfer (FRET) based technique (claim 27) to analyze the genome of a plant using PCR (claim 13). The method comprises PCR technique using fluorescent probes and the results are quantified by fluorescent plate readers (page 3, para 0034), which is a sensor to measure fluorescence. Raw fluorescence intensity data is analyzed directly from a plate reader using a suitable analysis package (page 3, para 0032). It is helpful to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent (page 3, para 0034-0035) and thus to significantly reduce cost and time in plant breeding projects (abstract).
It would have been obvious to one of ordinary skill in the art to modify the method, as described by Manley et al., to identify a sugar beet plant that is resistant or tolerant to Cercospora by using a fluorescent resonance energy transfer (FRET) based system, as taught by Manley et al. It is known and a standard practice in the art to detect presence or absence of a nucleotide sequence based on a set of at least two primers that hybridize within the target sequence. The artisan can use two (or more) forward primers aligning to different regions along the length of the target sequence while using a single reverse primer, to detect presence or absence of a specific target sequence. Use of a common reverse primer is within the experimental design choice of an ordinarily skilled artisan as it would have detected the presence of a specific target sequence. It would have been obvious to use FRET to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent and thus to significantly reduce cost and time in plant breeding projects, as described by Manley et al.
Before the effective filing date of the invention, one ordinarily skilled artisan would have been motivated to use two forward primers and a common reverse primer while using FRET with the realistic objective to remove linkage drag to reduce cost and time while developing Cercospora resistant plants in commercially important sugar beet varieties.
Claims 11-14 are rejected on the ground of nonstatutory double patenting as being unpatentable claims 1 and 11-12 of U.S. Patent No. US 10767191B1 to Törjék et al. in view of Singh et al. as applied to claims 1-2 and 5-8 above, and further in view of Czarnecki et al. (EP3628738 A1). This is a new rejection necessitated by the claim amendments.
Instant independent claim 11 is drawn to a plant of the genus Beta or Spinacia comprising a polynucleotide comprising instant SEQ ID NO: 2 encoding a polypeptide that is able to confer resistance to Cercospora, wherein the plant furthermore comprises an endogenous allele encoding an epsp synthase comprising instant SEQ ID NO: 223.
Claims 1 and 11-12 of Torjek et al. in view of Singh et al. describe a plant of the genus Beta (sugar beet) comprising a polynucleotide consisting of SEQ ID NO: 3 and/or functional equivalent(s) thereof encoding the polypeptide consisting of SEQ ID NO: 3, which is able to confer resistance to Cercospora, as discussed above.
However, Torjek et al. in view of Singh et al. do not teach an endogenous allele encoding an epsp synthase comprising the polypeptide of SEQ ID NO: 223.
Czarnecki et al. describes a method to control weeds in sugar beet (page 2, para 0001, line 1) cultivation. It describes producing an herbicide (glyphosate) resistant sugar beet plant comprising an endogenous allele encoding a mutant epsp synthase. It teaches an endogenous allele of epsp synthase (SEQ ID NO: 3) (claim 3; page 11, para 0050; page 19, para 0103, line 4-6) comprising 100% sequence identity to instant SEQ ID NO: 223, as shown below.
RESULT 1
BHN75224
ID BHN75224 standard; protein; 517 AA.
AC BHN75224;
DT 14-MAY-2020 (first entry)
DE Beta vulgaris mutant EPSPS (P179S), SEQ ID:3.
KW 5-enolpyruvylshikimate-3-phosphate synthase; Biofuel; EPSPS protein;
KW Plant; crop improvement; enzyme engineering; herbicide resistance;
KW mutein; sugar; weed control.
OS Beta vulgaris.
OS Synthetic.
FT Misc-difference 179
FT /note= "Wild-type Pro substituted by Ser"
CC PN EP3628738-A1.
CC PD 01-APR-2020.
CC PF 25-SEP-2018; 2018EP-00196607.
PR 25-SEP-2018; 2018EP-00196607.
CC PA (KWSS-) KWS SAAT SE & CO KGAA.
CC PI Czarnecki O, Gertz M, Lein JC, Wurbs D;
DR WPI; 2020-24524Y/031.
DR N-PSDB; BHN75222, BHN75223.
CC Controlling bolters in sugar beet growing areas, involves planting sugar
beet plants or sowing sugar beet seed comprising endogenous allele, and
applying glyphosate herbicide to growing plants.
CC PS Claim 3; SEQ ID NO 3; 76pp; English.
SQ Sequence 517 AA;
Query Match 100.0%; Score 2634; Length 517; Best Local Similarity 100.0%;
Matches 517; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
Qy 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
Qy 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
Qy 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
Qy 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
Qy 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
Qy 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
Qy 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
Qy 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
|||||||||||||||||||||||||||||||||||||
Db 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
Before the effective filing date, it would be obvious to an ordinarily skilled artisan to transform the Cercospora resistance beet plant, as described by Törjék et al., using art recognized CRISPR-Cas gene editing method to either replace the Cercospora susceptible endogenous epsp synthase allele with a polynucleotide sequence encoding the mutated epsp synthase protein or edit the endogenous esps synthase gene at specific codons that would have encoded the mutated allele of esps polypeptide as described by Czarnecki et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to introduce herbicide (glyphosate) resistance gene encoding a polypeptide comprising 100% sequence identity to SEQ ID NO: 223 into a commercially important sugar beet plant already having th Cercospora resistance trait.
Instant claim 12 is drawn to the plant according to claim 11, further characterized by a feature or a combination of features selected from the group consisting of: the plant is a hybrid and/or a double haploid plant; the resistance against Cercospora is dominant; the nucleic acid molecule or nucleotide sequence is comprised as an introgression or is comprised homozygous, and the plant has tolerance to glyphosate. Plant breeding method of making a hybrid and/or a double haploid plant and introducing any new trait1 including herbicide (e.g. glyphosate) resistance are well known and standard technique in the art.
Instant claim 13 recites a storage organ or a leaf of the plant according to claim 11. Sugar beet plants comprising Cercospora resistance and glyphosate resistant esps synthase gene, as described above, would have its leaves and the storage organ.
Instant claim 14 recites a pelleted seed of the plant according to claim 11. Claim 1 of Torjek et al. recites a pelleted seed of sugar beet.
Claims 1-2 and 5-8 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 17 of U.S. Patent No. 11597944B2 (hereafter referred to as ‘944). in view of Singh et al. (Primer Premier: Program for Design of Degenerate Primers from a Protein Sequence, 1998, BioTechniques 24:318-319).
Claim 1 of ‘944 recites, “A plant of the subspecies Beta vulgaris subsp. Vulgaris comprising a nucleic acid molecule encoding a polypeptide that is able to confer resistance to Cercospora beticola in a plant in which the polypeptide is expressed, characterized in that the nucleic acid molecule comprises a nucleotide sequence which is selected from the group consisting of:
(a) a nucleotide sequence that encodes a polypeptide having the amino acid sequence according to SEQ ID NO: 3; and
(b) a nucleotide sequence that encodes a polypeptide which has an amino acid sequence that is at least 95% identical to the amino acid sequence according to SEQ ID NO: 3.
SEQ ID NO: 3 of ‘944 is 100% identical to instant SEQ ID NO: 3 (data not sown). The plant of claim 1 of ‘944 would enable any ordinarily skilled artisan to use routine and standard method of introgression to develop plants including Beta vulgaris that are resistant or tolerant to Cercospora beticola.
Sugar beet is a known commercially important plant belonging to genus Beta, as recited in instant claim 8.
The claims of ‘944 do not explicitly recite a method of identifying a plant having a polynucleotide comprising at least 95% sequence identity to instant SEQ ID NO: 2 conferring resistance/tolerance to Cercospora by using oligonucleotide primers/markers.
Singh et al. teaches a technique to use degenerate primers comprising at least two oligonucleotides, as recited in instant claims 6-7, designed from a known protein sequence for successful detection (as recited in instant claim 5) of any DNA sequence encoding the protein comprising SEQ ID NO: 3 (page 319, last 2 para). Extraction of DNA from plant tissue(s), as recited in claim 5, is well known standard method in the art. Before the effective filing date of the invention, detecting presence or absence of a nucleotide sequence encoding a known protein using degenerate primers for PCR became well known in the art, as taught by Singh et al.
Before the effective filing date of the invention, it would have been obvious and within the scope of one of ordinary skill in the art to detect for the presence or absence of the nucleotide sequence encoding the polypeptide consisting of SEQ ID NO: 3 in a sugar beet plant, given that claim 1 of ‘944 teach that SEQ ID NO: 3 confers resistance to Cercospora beticola. It also would have been obvious to transform a sugar beet plant with a polynucleotide sequence encoding SEQ ID NO: 3, as described by claim 1 of ‘944, to develop a Cercospora resistant sugar beet plant. It would also have been obvious to detect for the presence or absence of the gene encoding SEQ ID NO: 3 in the plant, following well-known PCR methodologies such as the one taught by Singh et al. That would have been led to endogenous genomic DNA sequence comprising SEQ ID NO: 2 and/or allele(s), which is/are the functional equivalent(s) of the polypeptide comprising of SEQ ID NO: 3 and flanked by markers s4p1395s01 and s4p0421s01 (as recited in claim 7). These markers are inherently present in the endogenous gene. See the instant specification, Table 1B and the paragraph bridging p. 45-46 which teaches that these markers flank the genomic region which comprises the resistance gene. It’s crucial to note that it is the polypeptide, and not the polynucleotide encoding it, that confers Cercospora resistance. The polynucleotide sequences encoding the polypeptide consisting of SEQ ID NO: 3 are considered functional equivalents. Using and/or detecting any specific polynucleotide encoding a polypeptide consisting of SEQ ID NO: 3 is an experimental design choice of an ordinarily skilled artisan.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to identify a plant that is resistant/tolerant to Cercospora by detecting the presence or absence of a nucleotide sequence that encodes a polypeptide consisting of SEQ ID NO: 3 which is a functional equivalent of the DNA sequence having at least 95% identical to SEQ ID NO: 2 conferring resistance/tolerance to Cercospora.
Moreover, claim 17 of ‘944B, indirectly depends from claim 1 of ‘944B. Claim 17 of ‘944B recites a method for identifying a Cercospora beticola resistant plant of the subspecies Beta vulgaris subsp. Vulgaris. The plant comprises the nucleotide sequence that encodes a polypeptide comprising SEQ ID NO: 3, as recited in claim 1 of ‘944B.
Claims 9-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 11-12 of U.S. Patent No. 11597944B2 to Törjék et al., in view of Singh et al. as applied to claims 1-2 and 5-8 above, and further in view of Manley et al. (US 2014/0212877 A1).
Instant claim 9 depends from claim 1 and recites a method comprising a PCR step involving two allele-specific forward primers and wherein the detection step involves fluorescence resonant energy transfer and wherein the presence, absence or kind of the fluorescence is determined by a sensor. Instant claim 10 depends from claim 9 and requires the involvement of one common reverse primer.
Claims 1 of ‘944 et al. in view of Singh et al. describe a method of identifying a Cercospora resistance beet plant using PCT comprising forward and reverse primers to detect a polynucleotide comprising the SEQ ID NO: 2 or any functional equivalent of the DNA sequence having at least 95% identical to SEQ ID NO: 2 conferring resistance/ tolerance to Cercospora, as discussed above.
However, the claims 1 of ‘944 in view of Sing et al., do not describe fluorescent resonance energy transfer (FRET) based method and wherein the presence, absence or kind of the fluorescence is determined by a sensor.
Manley et al. describes the method of using fluorescent resonance energy transfer (FRET) based technique (claim 27) to analyze the genome of a plant using PCR (claim 13). The method comprises PCR technique using fluorescent probes and the results are quantified by fluorescent plate readers (page 3, para 0034), which is a sensor to measure fluorescence. Raw fluorescence intensity data is analyzed directly from a plate reader using a suitable analysis package (page 3, para 0032). It is helpful to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent (page 3, para 0034-0035) and thus to significantly reduce cost and time in plant breeding projects (abstract).
It would have been obvious to one of ordinary skill in the art to modify the method, as described by Manley et al., to identify a sugar beet plant that is resistant or tolerant to Cercospora by using a fluorescent resonance energy transfer (FRET) based system, as taught by Manley et al. It is known and a standard practice in the art to detect presence or absence of a nucleotide sequence based on a set of at least two primers that hybridize within the target sequence. The artisan can use two (or more) forward primers aligning to different regions along the length of the target sequence while using a single reverse primer, to detect presence or absence of a specific target sequence. Use of a common reverse primer is within the experimental design choice of an ordinarily skilled artisan as it would have detected the presence of a specific target sequence. It would have been obvious to use FRET to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent and thus to significantly reduce cost and time in plant breeding projects, as described by Manley et al.
Before the effective filing date of the invention, one ordinarily skilled artisan would have been motivated to use two forward primers and a common reverse primer while using FRET with the realistic objective to remove linkage drag to reduce cost and time while developing Cercospora resistant plants in commercially important sugar beet varieties.
Claims 11-14 are rejected on the ground of nonstatutory double patenting as being unpatentable claims 1 of U.S. Patent No. US11597944B2 to Törjék et al. in view of Singh et al. as applied to claims 1-2 and 5-8 above, and further in view of Czarnecki et al. (EP3628738 A1).
Instant independent claim 11 is drawn to a plant of the genus Beta or Spinacia comprising a polynucleotide comprising instant SEQ ID NO: 2 encoding a polypeptide that is able to confer resistance to Cercospora, wherein the plant furthermore comprises an endogenous allele encoding an epsp synthase comprising instant SEQ ID NO: 223.
Claims 1 of ‘944 in view of Singh et al. describe a plant of the genus Beta (sugar beet) comprising a polynucleotide consisting of SEQ ID NO: 2 and/or functional equivalent(s) thereof encoding the polypeptide consisting of SEQ ID NO: 3, which is able to confer resistance to Cercospora, as discussed above.
Claims 11-12 and 14 of ‘944 recite tolerance to at least one herbicide comprising glyphosate. Claim 14 of ‘944 explicitly recites 3 different SEQ ID NOs; SEQ ID NO: 83, SEQ ID NO: 86 and SEQ ID NO: 89. However, these sequences appear to be genomic sequences and none of the claims recite the polypeptide sequences encoded by any of the three glyphosate tolerance genes. Thus, it can not be determined if the proteins encoded by the three genomic DNA as 100% sequence identity to instant SEQ ID NO: 223.
‘944 in view of Singh et al. do not teach an endogenous allele encoding an epsp synthase comprising the polypeptide of SEQ ID NO: 223.
Czarnecki et al. describes a method to control weeds in sugar beet (page 2, para 0001, line 1) cultivation. It describes producing an herbicide (glyphosate) resistant sugar beet plant comprising an endogenous allele encoding a mutant epsp synthase. It teaches an endogenous allele of esps synthase (SEQ ID NO: 3) (claim 3; page 11, para 0050; page 19, para 0103, line 4-6) comprising 100% sequence identity to instant SEQ ID NO: 223, as shown below.
RESULT 1
BHN75224
ID BHN75224 standard; protein; 517 AA.
AC BHN75224;
DT 14-MAY-2020 (first entry)
DE Beta vulgaris mutant EPSPS (P179S), SEQ ID:3.
KW 5-enolpyruvylshikimate-3-phosphate synthase; Biofuel; EPSPS protein;
KW Plant; crop improvement; enzyme engineering; herbicide resistance;
KW mutein; sugar; weed control.
OS Beta vulgaris.
OS Synthetic.
FT Misc-difference 179
FT /note= "Wild-type Pro substituted by Ser"
CC PN EP3628738-A1.
CC PD 01-APR-2020.
CC PF 25-SEP-2018; 2018EP-00196607.
PR 25-SEP-2018; 2018EP-00196607.
CC PA (KWSS-) KWS SAAT SE & CO KGAA.
CC PI Czarnecki O, Gertz M, Lein JC, Wurbs D;
DR WPI; 2020-24524Y/031.
DR N-PSDB; BHN75222, BHN75223.
CC Controlling bolters in sugar beet growing areas, involves planting sugar
beet plants or sowing sugar beet seed comprising endogenous allele, and
applying glyphosate herbicide to growing plants.
CC PS Claim 3; SEQ ID NO 3; 76pp; English.
SQ Sequence 517 AA;
Query Match 100.0%; Score 2634; Length 517; Best Local Similarity 100.0%;
Matches 517; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
Qy 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
Qy 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
Qy 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
Qy 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
Qy 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
Qy 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
Qy 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
Qy 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
|||||||||||||||||||||||||||||||||||||
Db 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
Before the effective filing date, it would be obvious to an ordinarily skilled artisan to transform the Cercospora resistance beet plant, as recited in claim 1 of ‘944 using art recognized CRISPR-Cas gene editing method to either replace the Cercospora susceptible endogenous epsp synthase allele with a polynucleotide sequence encoding the mutated epsp synthase protein or edit the endogenous esps synthase gene at specific codons that would have encoded the mutated allele of esps polypeptide as described by Czarnecki et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to introduce herbicide (glyphosate) resistance gene encoding a polypeptide comprising 100% sequence identity to SEQ ID NO: 223 into a commercially important sugar beet plant already having the Cercospora resistance trait.
Instant claim 12 is drawn to the plant according to claim 11, further characterized by a feature or a combination of features selected from the group consisting of: the plant is a hybrid and/or a double haploid plant; the resistance against Cercospora is dominant; the nucleic acid molecule or nucleotide sequence is comprised as an introgression or is comprised homozygous, and the plant has tolerance to glyphosate. Plant breeding method of making a hybrid and/or a double haploid plant and introducing any new trait including herbicide (e.g. glyphosate) resistance are well known and standard technique in the art.
Instant claim 13 recites a storage organ or a leaf of the plant according to claim 11. Sugar beet plants comprising Cercospora resistance and glyphosate resistant esps synthase gene, as described above, would have its leaves and the storage organ.
Instant claim 14 recites a pelleted seed of the plant according to claim 11. Claim 1 of Torjek et al. recites a pelleted seed of sugar beet.
Claims 1-8 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 9-10 of U.S. Patent No. 12,098,377 B2 (hereafter referred to as ‘377) to Torjek et al. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of ‘377 recites, “A nucleic acid molecule which encodes a polypeptide that is able to confer resistance to Cercospora beticola in a Beta vulgaris subsp. vulgaris plant in which the polypeptide is expressed, wherein the nucleic acid molecule comprises the DNA sequence according to SEQ ID NO: 2”.
SEQ ID NO: 2 of ‘377 is 100% identical to instant SEQ ID NO: 2 (data not sown). The nucleotide sequence comprising SEQ ID NO: 2 of ‘377 would enable any ordinarily skilled artisan to use routine and standard method of plant transformation to develop plants that are resistant or tolerant to Cercospora beticola.
Sugar beet is a known commercially important plant belonging to genus Beta, as recited in instant claim 8.
Claims 9-10 of ‘377 are drawn to a method comprising sensitive allelic variant that comprises a nucleotide sequence which does not confer resistance to Cercospora beticola.
Designing PCR primers and other markers to detect polymorphism(s) including single nucleotide polymorphism(s) (SNPs), as recited in instant claims 3-4, is a routine and standard process in the art.
Claims 9-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 11-12 of U.S. Patent No. US 12,098,377 B2 to Törjék et al., as applied to claims 1-2 and 5-8 above, and further in view of Manley et al. (US 2014/0212877 A1).
Instant claim 9 depends from claim 1 and recites a method comprising a PCR step involving two allele-specific forward primers and wherein the detection step involves fluorescence resonant energy transfer and wherein the presence, absence or kind of the fluorescence is determined by a sensor. Instant claim 10 depends from claim 9 and requires the involvement of one common reverse primer.
SEQ ID NO: 2 of ‘377 is 100% identical to instant SEQ ID NO: 2 (data not sown). The nucleotide sequence comprising SEQ ID NO: 2 of ‘377 would enable any ordinarily skilled artisan to use routine and standard method of plant transformation to develop plants that are resistant or tolerant to Cercospora beticola.
However, none of the claims of ‘377 describe fluorescent resonance energy transfer (FRET) based method and wherein the presence, absence or kind of the fluorescence is determined by a sensor.
Manley et al. describes the method of using fluorescent resonance energy transfer (FRET) based technique (claim 27) to analyze the genome of a plant using PCR (claim 13). The method comprises PCR technique using fluorescent probes and the results are quantified by fluorescent plate readers (page 3, para 0034), which is a sensor to measure fluorescence. Raw fluorescence intensity data is analyzed directly from a plate reader using a suitable analysis package (page 3, para 0032). It is helpful to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent (page 3, para 0034-0035) and thus to significantly reduce cost and time in plant breeding projects (abstract).
It would have been obvious to one of ordinary skill in the art to modify the method, as described by Manley et al., to identify a sugar beet plant that is resistant or tolerant to Cercospora by using a fluorescent resonance energy transfer (FRET) based system, as taught by Manley et al. It is known and a standard practice in the art to detect presence or absence of a nucleotide sequence based on a set of at least two primers that hybridize within the target sequence. The artisan can use two (or more) forward primers aligning to different regions along the length of the target sequence while using a single reverse primer, to detect presence or absence of a specific target sequence. Use of a common reverse primer is within the experimental design choice of an ordinarily skilled artisan as it would have detected the presence of a specific target sequence. It would have been obvious to use FRET to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent and thus to significantly reduce cost and time in plant breeding projects, as described by Manley et al.
Before the effective filing date of the invention, one ordinarily skilled artisan would have been motivated to use two forward primers and a common reverse primer while using FRET with the realistic objective to remove linkage drag to reduce cost and time while developing Cercospora resistant plants in commercially important sugar beet varieties.
Claims 11-14 are rejected on the ground of nonstatutory double patenting as being unpatentable claims 1 of U.S. Patent No. 12,098,377 B2 to Törjék et al. as applied to claims 1-2 and 5-8 above, and further in view of Czarnecki et al. (EP3628738 A1).
Instant independent claim 11 is drawn to a plant of the genus Beta or Spinacia comprising a polynucleotide comprising at least 95% sequence identity to instant SEQ ID NO: 2 encoding a polypeptide that is able to confer resistance to Cercospora, wherein the plant furthermore comprises an endogenous allele encoding an epsp synthase comprising instant SEQ ID NO: 223.
Claims 1 of ‘944 in view of Singh et al. describe a plant of the genus Beta (sugar beet) comprising a polynucleotide consisting of SEQ ID NO: 2 and/or functional equivalent(s) thereof encoding the polypeptide consisting of SEQ ID NO: 3, which is able to confer resistance to Cercospora, as discussed above.
Claims 11-12 and 14 of ‘944 recite tolerance to at least one herbicide comprising glyphosate. Claim 14 of ‘944 explicitly recites 3 different SEQ ID NOs; SEQ ID NO: 83, SEQ ID NO: 86 and SEQ ID NO: 89. However, these sequences appear to be genomic sequences and none of the claims recite the polypeptide sequences encoded by any of the three glyphosate tolerance genes. Thus, it can not be determined if the proteins encoded by the three genomic DNA as 100% sequence identity to instant SEQ ID NO: 223.
‘944 in view of Singh et al. do not teach an endogenous allele encoding an epsp synthase comprising the polypeptide of SEQ ID NO: 223.
Czarnecki et al. describes a method to control weeds in sugar beet (page 2, para 0001, line 1) cultivation. It describes producing an herbicide (glyphosate) resistant sugar beet plant comprising an endogenous allele encoding a mutant epsp synthase. It teaches an endogenous allele of esps synthase (SEQ ID NO: 3) (claim 3; page 11, para 0050; page 19, para 0103, line 4-6) comprising 100% sequence identity to instant SEQ ID NO: 223, as shown below.
RESULT 1
BHN75224
ID BHN75224 standard; protein; 517 AA.
AC BHN75224;
DT 14-MAY-2020 (first entry)
DE Beta vulgaris mutant EPSPS (P179S), SEQ ID:3.
KW 5-enolpyruvylshikimate-3-phosphate synthase; Biofuel; EPSPS protein;
KW Plant; crop improvement; enzyme engineering; herbicide resistance;
KW mutein; sugar; weed control.
OS Beta vulgaris.
OS Synthetic.
FT Misc-difference 179
FT /note= "Wild-type Pro substituted by Ser"
CC PN EP3628738-A1.
CC PD 01-APR-2020.
CC PF 25-SEP-2018; 2018EP-00196607.
PR 25-SEP-2018; 2018EP-00196607.
CC PA (KWSS-) KWS SAAT SE & CO KGAA.
CC PI Czarnecki O, Gertz M, Lein JC, Wurbs D;
DR WPI; 2020-24524Y/031.
DR N-PSDB; BHN75222, BHN75223.
CC Controlling bolters in sugar beet growing areas, involves planting sugar
beet plants or sowing sugar beet seed comprising endogenous allele, and
applying glyphosate herbicide to growing plants.
CC PS Claim 3; SEQ ID NO 3; 76pp; English.
SQ Sequence 517 AA;
Query Match 100.0%; Score 2634; Length 517; Best Local Similarity 100.0%;
Matches 517; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
Qy 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
Qy 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
Qy 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
Qy 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
Qy 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
Qy 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
Qy 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
Qy 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
|||||||||||||||||||||||||||||||||||||
Db 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
Before the effective filing date, it would be obvious to an ordinarily skilled artisan to transform the Cercospora resistance beet plant, as described by Törjék et al., using art recognized CRISPR-Cas gene editing method to either replace the Cercospora susceptible endogenous epsp synthase allele with a polynucleotide sequence encoding the mutated epsp synthase protein or edit the endogenous esps synthase gene at specific codons that would have encoded the mutated allele of esps polypeptide as described by Czarnecki et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to introduce herbicide (glyphosate) resistance gene encoding a polypeptide comprising 100% sequence identity to SEQ ID NO: 223 into a commercially important sugar beet plant already having the Cercospora resistance trait.
Instant claim 12 is drawn to the plant according to claim 11, further characterized by a feature or a combination of features selected from the group consisting of: the plant is a hybrid and/or a double haploid plant; the resistance against Cercospora is dominant; the nucleic acid molecule or nucleotide sequence is comprised as an introgression or is comprised homozygous, and the plant has tolerance to glyphosate. Plant breeding method of making a hybrid and/or a double haploid plant and introducing any new trait including herbicide (e.g. glyphosate) resistance are well known and standard technique in the art.
Instant claim 13 recites a storage organ or a leaf of the plant according to claim 11. Sugar beet plants comprising Cercospora resistance and glyphosate resistant esps synthase gene, as described above, would have its leaves and the storage organ.
Instant claim 14 recites a pelleted seed of the plant according to claim 11. Claim 1 of Torjek et al. recites a pelleted seed of sugar beet.
Claims 1-2 and 5-8 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 18/161,613 (hereafter referred to as ‘613). Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of ‘613 recites, “a plant of the subspecies Beta vulgaris subsp. vulgaris comprising a nucleic acid molecule encoding a polypeptide that is able to confer resistance to Cercospora beticola in a plant in which the polypeptide is expressed, wherein the nucleic acid molecule comprises a nucleotide sequence which is selected from the group consisting of:
(a) a nucleotide sequence that comprises the DNA sequence according to SEQ ID NO: 2;
(b) a nucleotide sequence that comprises the DNA sequence according to SEQ ID NO: 1 or SEQ ID NO: 53; and
(c) a nucleotide sequence that is at least 95% identical to the DNA sequence according to SEQ ID NO: 1 or SEQ ID NO: 2.
SEQ ID NO: 2 of ‘613 is 100% identical to instant SEQ ID NO: 2 (data not sown). The plant of claim 1 of ‘613 would enable any ordinarily skilled artisan to use routine and standard methods including PCR to identify plants that are resistant or tolerant to Cercospora beticola by detecting the presence of absence of SEQ ID NO: 2, as recited in claim 1 of ‘613. Extraction of DNA from a plant tissue, designing PCR primers and other markers to detect polymorphism(s), as recited in instant claims 1 and 5-7, are routine and standard processes in the art.
Sugar beet is a known commercially important plant belonging to genus Beta, as recited in instant claim 8.
Claim 9-10 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 of copending Application No. 18/161,613 (reference application) as applied to claims 1-2 and 5-8 above, and further in view of Manley et al. (US 2014/0212877 A1).
Instant claim 9 depends from claim 1 and recites a method comprising a PCR step involving two allele-specific forward primers and wherein the detection step involves fluorescence resonant energy transfer and wherein the presence, absence or kind of the fluorescence is determined by a sensor. Instant claim 10 depends from claim 9 and requires the involvement of one common reverse primer.
Claims 1 of ‘613 makes the method of identifying a Cercospora resistance beet plant using PCT comprising forward and reverse primers to detect a polynucleotide comprising the SEQ ID NO: 2 conferring resistance/ tolerance to Cercospora obvious, as discussed above.
However, the claims 1 of ‘613 does not describe fluorescent resonance energy transfer (FRET) based method and wherein the presence, absence or kind of the fluorescence is determined by a sensor.
Manley et al. describes the method of using fluorescent resonance energy transfer (FRET) based technique (claim 27) to analyze the genome of a plant using PCR (claim 13). The method comprises PCR technique using fluorescent probes and the results are quantified by fluorescent plate readers (page 3, para 0034), which is a sensor to measure fluorescence. Raw fluorescence intensity data is analyzed directly from a plate reader using a suitable analysis package (page 3, para 0032). It is helpful to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent (page 3, para 0034-0035) and thus to significantly reduce cost and time in plant breeding projects (abstract).
It would have been obvious to one of ordinary skill in the art to modify the method, as described by Manley et al., to identify a sugar beet plant that is resistant or tolerant to Cercospora by using a fluorescent resonance energy transfer (FRET) based system, as taught by Manley et al. It is known and a standard practice in the art to detect presence or absence of a nucleotide sequence based on a set of at least two primers that hybridize within the target sequence. The artisan can use two (or more) forward primers aligning to different regions along the length of the target sequence while using a single reverse primer, to detect presence or absence of a specific target sequence. Use of a common reverse primer is within the experimental design choice of an ordinarily skilled artisan as it would have detected the presence of a specific target sequence. It would have been obvious to use FRET to identify and remove linkage drag, i.e., the part of the chromosome which is not homozygous for the elite parent and thus to significantly reduce cost and time in plant breeding projects, as described by Manley et al.
Before the effective filing date of the invention, one ordinarily skilled artisan would have been motivated to use two forward primers and a common reverse primer while using FRET with the realistic objective to remove linkage drag to reduce cost and time while developing Cercospora resistant plants in commercially important sugar beet varieties.
Claim 11-14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 24-25 and 27 of copending Application No. 18/161,613 (reference application) and further in view of Czarnecki et al. (EP3628738 A1).
Instant independent claim 11 is drawn to a plant of the genus Beta or Spinacia comprising a polynucleotide comprising instant SEQ ID NO: 2 encoding a polypeptide that is able to confer resistance to Cercospora, wherein the plant furthermore comprises an endogenous allele encoding an epsp synthase comprising instant SEQ ID NO: 223.
Claims 24-25 of ‘613 are drawn to a plant having tolerance to at least one herbicide comprising glyphosate. Claim 27 of ‘613 explicitly recites glyphosate tolerant plants having one of the 3 different SEQ ID NOs; SEQ ID NO: 83, SEQ ID NO: 86 and SEQ ID NO: 89. However, these sequences appear to be genomic sequences and none of the claims recite the polypeptide sequences encoded by any of the three glyphosate tolerance genes. Thus, it cannot be determined if the proteins encoded by the three genomic DNA as 100% sequence identity to instant SEQ ID NO: 223.
Czarnecki et al. describes a method to control weeds in sugar beet (page 2, para 0001, line 1) cultivation. It describes producing an herbicide (glyphosate) resistant sugar beet plant comprising an endogenous allele encoding a mutant epsp synthase. It teaches an endogenous allele of esps synthase (SEQ ID NO: 3) (claim 3; page 11, para 0050; page 19, para 0103, line 4-6) comprising 100% sequence identity to instant SEQ ID NO: 223, as shown below.
RESULT 1
BHN75224
ID BHN75224 standard; protein; 517 AA.
AC BHN75224;
DT 14-MAY-2020 (first entry)
DE Beta vulgaris mutant EPSPS (P179S), SEQ ID:3.
KW 5-enolpyruvylshikimate-3-phosphate synthase; Biofuel; EPSPS protein;
KW Plant; crop improvement; enzyme engineering; herbicide resistance;
KW mutein; sugar; weed control.
OS Beta vulgaris.
OS Synthetic.
FT Misc-difference 179
FT /note= "Wild-type Pro substituted by Ser"
CC PN EP3628738-A1.
CC PD 01-APR-2020.
CC PF 25-SEP-2018; 2018EP-00196607.
PR 25-SEP-2018; 2018EP-00196607.
CC PA (KWSS-) KWS SAAT SE & CO KGAA.
CC PI Czarnecki O, Gertz M, Lein JC, Wurbs D;
DR WPI; 2020-24524Y/031.
DR N-PSDB; BHN75222, BHN75223.
CC Controlling bolters in sugar beet growing areas, involves planting sugar
beet plants or sowing sugar beet seed comprising endogenous allele, and
applying glyphosate herbicide to growing plants.
CC PS Claim 3; SEQ ID NO 3; 76pp; English.
SQ Sequence 517 AA;
Query Match 100.0%; Score 2634; Length 517; Best Local Similarity 100.0%;
Matches 517; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAQASTINNGVKSTQLCPNLPKTHLSKSSKSVKFGSNLRFSPKLKSFNNERVGGNSSVVF 60
Qy 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RVRASVAAAAEKSSTVPEIVLQPIKEISGTIQLPGSKSLSNRILLLAALSQGTTVVDNLL 120
Qy 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YSDDIRYMLDALRTLGLNVEDDNIAKRAIVEGCGGLFPVGKDGKEIELFLGNAGTAMRSL 180
Qy 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TAAVAVAGGNSSYVLDGVPRMRERPIGDLVAGLKQLGADVDCYLGTNCPPVRVNAKGGLP 240
Qy 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGKVKLSGSVSSQYLTALLMATPLGLGDVEVEIIDKLISVPYVEMTIKLMERFGVSVEHS 300
Qy 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ADWGRFLIRGGQKYKSPGNAYVEGDASSASYFIGGAAVTGGTVTVEGCGTSSLQGDVKFA 360
Qy 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 EVLEKMGCKVSWTENSVTVTGPPRDASGRKHLRAVDVNMNKMPDVAMTLAVVALYADGPT 420
Qy 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TIRDVASWRVKETERMIAICTELRKLGATVEEGSDYCVITPPEKLNVTAIDTYDDHRMAM 480
Qy 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
|||||||||||||||||||||||||||||||||||||
Db 481 AFSLAACADVPVTIKDPGCTRKTFPDYFDVLERFAKH 517
Before the effective filing date, it would be obvious to an ordinarily skilled artisan to transform the Cercospora resistance beet plant, as recited in claim 1 of ‘944 using art recognized CRISPR-Cas gene editing method to either replace the Cercospora susceptible endogenous epsp synthase allele with a polynucleotide sequence encoding the mutated epsp synthase protein or edit the endogenous esps synthase gene at specific codons that would have encoded the mutated allele of esps polypeptide as described by Czarnecki et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to introduce herbicide (glyphosate) resistance gene encoding a polypeptide comprising 100% sequence identity to SEQ ID NO: 223 into a commercially important sugar beet plant already having the Cercospora resistance trait.
Instant claim 12 is drawn to the plant according to claim 11, further characterized by a feature or a combination of features selected from the group consisting of: the plant is a hybrid and/or a double haploid plant; the resistance against Cercospora is dominant; the nucleic acid molecule or nucleotide sequence is comprised as an introgression or is comprised homozygous, and the plant has tolerance to glyphosate. Plant breeding method of making a hybrid and/or a double haploid plant and introducing any new trait including herbicide (e.g. glyphosate) resistance are well known and standard technique in the art.
Instant claim 13 recites a storage organ or a leaf of the plant according to claim 11. Sugar beet plants comprising Cercospora resistance and glyphosate resistant esps synthase gene, as described above, would have its leaves and the storage organ.
Instant claim 14 recites a pelleted seed of the plant according to claim 11. Claim 1 of Torjek et al. recites a pelleted seed of sugar beet.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1Afzal et al. (Seed Production Technologies of Some Major Field Crops. In: Hasanuzzaman, M. (eds) Agronomic Crops. Springer, Singapore. 2019) provides the evidence that making a hybrid plant and introducing any new trait including herbicide like glyphosate resistance is a well known and routine method in the art (page 671-672, para 28.8.4).
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