Status of the Claims
Amendments submitted on 04/30/2026 have been entered.
Claim 8 is canceled without prejudice and claims 1-4, 6, 11, 12, and 15 are amended.
Claims 1-7, 15, 19-21, & 23 are pending and are examined herein.
Status of Objections and Rejections
All previous objections and rejections not set forth below have been withdrawn in view of Applicant’s amendments and/or upon further consideration.
The text of those sections of Title 35 U.S. Code, not included in this action, can be found in a prior Office action.
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.
Claim 4 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. Parent claim 3 recites a method comprising "an amino acid sequence encoded by a nucleic acid sequence which is at least 95%, … identical to the nucleic acid sequence as shown in any one of SEQ ID NOs: 1, 4, 42 and 44,". Dependent claim 4 recites in part I alternative b "an amino acid sequence encoded by a nucleic acid sequence which is at least 90%... identical to the nucleic acid sequence as shown in any one of SEQ ID NO: 4" and in part II alternative b "an amino acid sequence encoded by a nucleic acid sequence which is at least 90%… identical to the nucleic acid sequence as shown in any one of SEQ ID NO: 44", which encompass sequences that fall outside of the scope recited in claim 3 (i.e., at least 95%, … identical). Thus, claim 4 fails to further limit the subject matter and to include all the limitations of claim 3. 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 § 103
Claims 1, 2 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Larkan (Larkan et al (2020), The Brassica napus wall-associated kinase-like (WAKL) gene Rlm9 provides race-specific blackleg resistance. Plant J., 104: 892-900. https://doi.org/10.1111/tpj.14966. published 07/14/2020) in view of NCBI accession AAL61927.1 (made available on NCBI by 01/20/2002), NCBI accession XM_018589549.1 (made available on NCBI by 06/14/2016), and NCBI accession AOIX01018552.1 (made available on NCBI by 03/28/2014).
Regarding claims 1 , Larkan teaches that “the Brassica R genes Rlm3, Rlm4, Rlm7 and Rlm9 confer race-specific resistance against blackleg disease caused by L. Maculans [and] form a tight genetic cluster [at approximately 16 Mb] on chromosome A07 and may possibly be allelic variants of the same R locus” (p893, col 1, para 2-3). Larkan also teaches that “Rlm9 encodes a wall-associated kinase-like protein”(WAKL), “showing the highest homology to A. thaliana WAKL10 (At1g79680, 69% amino acid identity). (p893, col 1-2, para 3). Larkan teaches a method of producing blackleg resistant transgenic plants by transferring Rlm9, a WAKL10-homologous gene, into susceptible brassica napus plants (i.e., introducing into the genome of a plant at least one polynucleotide comprising a blackleg resistance locus or blackleg resistance associated open reading frame, wherein said plant is a Brassicaceae plant).
Larkan does not explicitly teach nucleic acid sequences which are at least 80% identical to the nucleic acid sequences shown in SEQ ID NO: 1.
NCBI Accession AAL61927.1 teaches the amino acid identity of A. thaliana WAKL10 (At1g79680).
NCBI Accession AAL61927.1 does not explicitly teach nucleic acid sequences which are at least 90% identical to the nucleic acid sequences of SEQ ID NO: 1.
However, NCBI Accession XM_018589549.1 is the downstream product of whole genome sequencing and teaches a predicted mRNA sequence in Raphanus sativus encoding a “wall-associated receptor kinase-like 10”(WAKL10) and NCBI blast of the At1g79680 encoded amino acid sequence (NCBI Accession AAL61927.1) against brassica genomes including Raphanus sativus teaches that XP_018445051.1 shows 71.14% homology with it (( see red arrow in annotation below).
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XP_018445051.1 is 91.66% (i.e., at least 90% ) identical to the sequence of SEQ ID NO: 1 (data not shown). Raphanus sativus and Brassica napus are both members of the Brassicaceae family, which includes various vegetables and oilseed. Additionally, NCBI Accession XP_018445051.1 is the peptide derived from XM_018589549.1 and teaches a peptide sequence that is 83.29% (i.e., at least 80% ) identical to the amino acid sequence of SEQ ID NO: 43 (data not shown). XM_018589549.1 is located in the 17 MB region (see the annotation below) of the scaffold produced by whole genome sequencing (WGS), a method that typically produces contiguous chromosomes.
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NCBI tblastn of the At1g79680 encoded amino acid sequence (NCBI Accession AAL61927.1) against brassica WGS data sets, including that of Brassica oleracea, teaches that nucleotide translation of AOIX01018552.1 (Brassica oleracea var. capitata cultivar line 02-12 Scaffold000115_66, whole genome shotgun sequence) shows 76.16% homology with it (data not shown). AOIX01018552.1 also shares 94% identity with XM_018589549.1 (see snippet below).
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AOIX01018552.1 shares 94.58% identity with nt 2106 to 9496 of SEQ ID NO: 1 (i.e., claim 1 part c, 15ic, ), and 94.57 identity with SEQ ID NO: 1 (i.e., claim 1 part b, Claim 15ib ),
Therefore, it would have been obvious to one of ordinary skill in the art before the filing of the claimed invention to combine the teachings of Larkan with the whole genome sequence of Raphanus sativus and to occur upon the instant invention because:
Larkan teaches identifying brassica genes “showing the highest homology to A. thaliana WAKL10 (At1g79680…).”
NCBI blast of the At1g79680 encoded amino acid sequence (NCBI Accession AAL61927.1) against brassica genomes including Raphanus sativus teaches that XP_018445051.1 shows 71.14% homology with it and is a predicted WAKL10.
NCBI tblastn of the At1g79680 encoded amino acid sequence (NCBI Accession AAL61927.1) against brassica WGS data sets, including that of Brassica oleracea, teaches that nucleotide translation of AOIX01018552.1 (Brassica oleracea var. capitata cultivar line 02-12 Scaffold000115_66, whole genome shotgun sequence) shows 76.16% homology with it.
Larkan also teaches transferring an identified At1g79680-highly-homologous gene into a Brassicaceae plant genome to create transgenic plants resistant to blackleg.
Larkan also suggests that “with the cloning of Rlm9 and the characterisation of the gene as a WAKL we now have the basis for possibly identifying the other three blackleg R genes within the Rlm3/4/7/9 cluster, co-located on chromosome A07 (page 897, para 2). One would have been motivated to this based on the above teachings and suggestion in order to Identify the sequence of other blackleg resistance genes and more efficiently introduce them into desirable but susceptible cultivars as did Larkan.
Regarding claim 2, which depends from claim 1 with the further limitation that the method comprise the introduction of a first polynucleotide having at least 90% identical to the nucleic acid sequence SEQ ID NO: 4 and a second polynucleotide having at least 90% identical to the nucleic acid sequence SEQ ID NO: 44, of AOIX01018552.1 teaches a polynucleotide having a nucleic acid sequence which is 90.39% and 94.16% (i.e., at least 90%) identical to the nucleic acid sequences of SEQ ID NO: 4 and SEQ ID NO: 44, respectively (see snippet above). Further, gene stacking was well known in the art at the time of filing.
Regarding claim 5, Larkan teaches the use of droplet digital PCR (ddPCR) in assessing insertion copy number in the T0 and “T1 plants derived from the transgenic line NLA68” (i.e., identifying a plant having integrated into its genome the polynucleotide comprising the blackleg resistance locus) and that a T1 plant carrying the insertion was self-fertilized to produce T2 seed the plants which showed stable expression of the Rlm9 resistance phenotype (i.e., generating progeny from said plant wherein blackleg resistance has been conferred to said progeny) ( page 893, col 2, para 2).
Claims 6-7 are rejected under 35 U.S.C. 103 as being unpatentable over Larkan in view of NCBI accession AAL61927.1, NCBI accession XM_018589549.1, and NCBI accession AOIX01018552.1 as applied to claims 1-2 and 5 above, and further in view of Menz (Menz J, Modrzejewski D, Hartung F, Wilhelm R, Sprink T. Genome Edited Crops Touch the Market: A View on the Global Development and Regulatory Environment. Front Plant Sci. 2020 Oct 9;11:586027. doi: 10.3389/fpls.2020.586027. PMID: 33163013; PMCID: PMC7581933, published 9/10/2020) and Jacqueth (U.S. Patent Application Publication No. 2021/0040569A1, assigned to Pioneer Hi Bred International Inc titled 'Methods of identifying, selecting, and producing disease resistant crops', published 2/11/2021).
Claim 6 is drawn to a method of conferring blackleg resistance to a plant comprising genetically modifying an allele of a gene of said plant which does not confer blackleg resistance into an allele comprising a Rlm3 associated reading frame which is capable of expressing a polypeptide comprising an amino acid sequence selected from an amino acid sequence encoded by a nucleic acid sequence which is at least 90% … identical to the nucleic acid sequence as shown in any one of SEQ ID NOs: 1, 4, 42 and 44;wherein said polypeptide is capable of conferring blackleg resistance to a plant.
Claim 7 depends from claim 6 with the further limitation that homologous recombination or a genome editing technology is used.
Combined modification of Larkan with NCBI accessions XM_018589549.1, XP_018445051.1, AAL61927.1, and AOIX01018552.1 teaches a nucleic acid sequence which is at least 90% … identical to the nucleic acid sequence as shown in SEQ ID NOs: 1, 4, 42 and 44 and suggests that the amino acid encoded there from is capable of conferring blackleg resistance to a plant, absent evidence to the contrary (see rejections of claims 1, 2 and 5).
Larkan and NCBI accessions XM_018589549.1, XP_018445051.1, AAL61927.1, and AOIX01018552.1 do not explicitly teach homologous recombination or a genome editing technology.
Menz teaches that resistant genome-edited (GE) plants are being differentially regulated, with many, though not all countries creating specific rules or exemptions for GE crops that do not introduce transgenes that exclude them from GMO legislation (page 13, conclusion). This distinction allows some GE crops, especially those without foreign DNA (transgenes), to reach the market faster.
Jacqueth, is in the same field of endeavor to produce disease resistant crops and aims to solve a reasonable pertinent problem as Applicant: introducing resistance genes into plants at a targeted location. Jacqueth teaches that “Disease affecting canola plants include, but are not limited …black leg;” (para 0026). Jacqueth teaches that “polynucleotide compositions can be introduced into the genome of a plant using genome editing technologies…. For example, the identified polynucleotides can be introduced into a desired location in the genome of a plant through the use of double-stranded break technologies such as TALENs, meganucleases, zinc finger nucleases, CRISPR-Cas, and the like” (i.e., genome editing) (para 0155). Jacqueth teaches homologous recombination by “replacing a native allele with a resistant allele” using a gRNA/Cas9 Site directed nuclease system where resistant alleles included, but were not limited to, wall associated kinases as in the present application (begins para 0171, example 6). This reads on genetically modifying an allele of a gene of said plant which does not confer blackleg resistance into an allele comprising a Rlm3 associated reading frame which is capable of expressing a polypeptide comprising an amino acid sequence selected from an amino acid sequence encoded by a nucleic acid sequence which is at least 90% … identical to the nucleic acid sequence as shown in any one of SEQ ID NOs: 1, 4, 42 and 44;wherein said polypeptide is capable of conferring blackleg resistance to a plant; wherein genome editing is used.
Therefore, it would have been obvious to one of ordinary skill in the art before the filing of the claimed invention to combine and modify the teachings of Larkan and NCBI accessions XM_018589549.1, XP_018445051.1, and AAL61927.1 with the method of homologous recombination taught by Jacqueth to genetically modify a native allele which may be an “an allele of said plant which does not confer blackleg resistance” (Instant application specification, page 21, lines 1-3) by introduce the open reading frame of a gene that confers enhanced resistance to blackleg using homologous recombination or a genome editing technology. There is a reasonable expectation of success of combining Larkan and NCBI accessions XM_018589549.1, XP_018445051.1, and AAL61927.1 with the method of homologous recombination taught by Jacqueth because Homologous recombination or homology direct repair is well known in the art. Homologous recombination and general genome editing techniques have been widely understood and used in genetic engineering field for decades, long before recent advancements like CRISPR made them more efficient. A person of ordinary skill in the art would be familiar with these methods. Additionally, Jacqueth was already teaching that their method was sell-suited for providing plant resistance to various diseases including but not limited to diseases affecting canola including blackleg. A person having ordinary skill in the art would have been motivated to combine and modify the above teachings to achieve the claimed invention as Menz teaches that “in November 2018, the delegations of several countries signed the international statement on agricultural applications of precision biotechnology in the WTO Committee on Sanitary and Phytosanitary Measures (CSPM)… agree[ing] to engage for the exploration of science based opportunities for regulatory frameworks and the avoidance of trade barriers for products derived from genome editing [and]… affirming that cultivars derived from genome editing should be regulated similar to conventional cultivars due to their high similarity” which created a perceivably lucrative market opportunity (page 13, WTO: Committee on Sanitary and Phytosanitary Measures).
Claim(s) 15, 19-21, and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Larkan in view of NCBI accession AAL61927.1, NCBI accession XM_018589549.1, and NCBI accession AOIX01018552.1 as applied to claims 1-2 and 5 above, and further in view of Wang (Wang et al. "Constitutive expression of pea defense gene DRR206 confers resistance to blackleg (Leptosphaeria maculans) disease in transgenic canola (Brassica napus)." Molecular plant-microbe interactions 12.5 (1999): 410-418., Published 01/26/1999).
Regarding claim 15, combined modification of Larkan with NCBI accessions XM_018589549.1, XP_018445051.1, AAL61927.1, and AOIX01018552.1 teaches a nucleic acid sequence which is at least 90% … identical to the nucleic acid sequence as shown in SEQ ID NOs: 1, 4, 42 and 44 and suggests that the amino acid encoded there from is capable of conferring blackleg resistance to a plant, absent evidence to the contrary (see rejections of claims 1, 2 and 5).
But Larkan and NCBI accessions XM_018589549.1, XP_018445051.1, AAL61927.1, and AOIX01018552.1 do not explicitly teach that said polynucleotide is operably linked to a heterologous promoter.
Wang, with the analogous goal of ascertaining blackleg disease resistance in a Brassicaceae plant, teaches “that constitutive expression of pea DRR206 [a known antifungal defense gene] can confer substantial resistance to blackleg, caused by L. maculans, in transgenic B. napus” (Abstract; page 411, para 1). Wang’s constitutive expression of the blackleg resistance gene is by the cauliflower mosaic virus (CaMV) 35S promoter which is not native to the DRR230 gene (i.e., said polynucleotide capable of conferring blackleg resistance to a plant is operably linked to a heterologous promoter). Additionally, Wang states that “disease resistance is correlated with strong expression of [blackleg resistance gene]” (page 412, Disease resistance is correlated with strong expression of pea DRR206 and defensin).
Therefore, it would have been obvious to one of ordinary skill in the art before the filing of the claimed invention to combine and modify the teachings of Larkan, and NCBI accessions XM_018589549.1, XP_018445051.1, and AAL61927.1 with Wang’s use of a heterologous promoter to substitute a heterologous promoter like CaMV 35S for the native promoter arriving at the instant invention of claim 15. The motivation to do this would come from Wang’s assertion that “disease resistance is correlated with strong expression of [blackleg resistance gene]” (page 412, Disease resistance is correlated with strong expression of pea DRR206 and defensin) and that CaMV 35S promoter is a strong constitutive promoter well known in the art.
Regarding claim 19, Wang teaches that the blackleg resistance gene DRR230 was “cloned into T-DNA–based binary vector pBI121 downstream from the constitutive CaMV 35S promoter, replacing the β-glucuronidase (GUS) gene” (page 411, Results, para 1). The resulting construct contained blackleg resistance gene DRR230 operably linked to a CaMV 35S promoter (i.e., a vector or gene construct comprising said polynucleotide, capable of conferring blackleg resistance to a plant, operably linked to a heterologous promoter).
Regarding claim 20, Wang teaches “35S-defense gene plasmid constructs were transfected into A. tumefaciens MP90 by the freeze-thaw method”(page 415, Materials and methods, para 1). The vector transfected A. tumefaciens and T1 and T2 transgenic plants contained or comprised blackleg resistance gene DRR230 operably linked to a CaMV 35S promoter (i.e., host cells comprising said polynucleotide, capable of conferring blackleg resistance to a plant, operably linked to a heterologous promoter).
Regarding claim 21, Wang’s T1 and T2 transgenic plants contained or comprised blackleg resistance gene DRR230 operably linked to a CaMV 35S promoter (i.e., plants comprising said polynucleotide, capable of conferring blackleg resistance to a plant, operably linked to a heterologous promoter).
Regarding claim 23, Wang teaches that “the expression of the DRR206 protein was verified by immunoblot” (page 413, col 2; fig 3). The blackleg resistance associated “proteins from Brassica napus transgenic lineGN3-4#22 T1 and T2 plants” read on a polypeptide encoded by the polynucleotide, capable of conferring blackleg resistance to a plant, operably linked to a heterologous promoter. Still, without explicit disclosure of the final polypeptide, a person skilled in the art would inevitably obtain the claimed polypeptide by practicing prior art references’ teachings if the references contain all the necessary elements as Larkan, and NCBI accessions XM_018589549.1, XP_018445051.1, and AAL61927.1 in view of Wang do.
Response to Applicant’s Arguments
Initially, it is noted that this is a new rejection necessitated by the claim amendments.
Without acquiescing to the correctness of the rejections, Applicant amended the claims to recite an increased percent identity and then argue that the combination of cited references does not teach or suggest every claim element of the amended claims (see table on page 10 of Remarks).
Nevertheless, due to the applicant’s amendments and the necessitated new references cited by the examiner, the arguments are moot.
Subject Matter Free of Prior Art
Claims 3-4 are deemed free of prior at, given the failure of the prior art to teach:
an amino acid sequence which is at least 95%... identical to the amino acid sequence shown in any one of SEQ ID NOs: 5, 43 and 45, wherein said polypeptide is capable of conferring blackleg resistance to a plant or
an amino acid sequence encoded by a nucleic acid sequence which is at least 95%, at least 96%, at least 97%… identical to the nucleic acid sequence as shown in any one of SEQ ID NOs: 1, 4, 42 and 44, wherein said polypeptide is capable of conferring blackleg resistance to a plant.
Conclusion
Claims 1-2, 4-7, 15, 19-21, and 23 are rejected.
Claim 3 is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YVETTE B TAMUKONG whose telephone number is (571)272-1040. The examiner can normally be reached M-Th 730-5 EST.
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/YVETTE TAMUKONG/ Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/ Supervisory Patent Examiner, Art Units 1661 & 1662
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