DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Applicant’s claim for the benefit of a prior-filed application filed 08/04/2023 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Thus, the earliest possible priority for the instant application is August 4, 2023.
Information Disclosure Statement
Initialed and dated copy of Applicant’s information disclosure statement (IDS) filed on 11/25/2024 is attached to the instant Office Action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code in ¶ 0033 of the Summary and in ¶ 0033 of the Detailed Description. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claims
Claims 1-15 are pending and are examined in this Office Action.
Claim Interpretation
Claim 12 recites a method of treating or preventing peanut smut infestation in a geographic region in need thereof, comprising: identifying a line of smut resistant peanuts, wherein at least one peanut from the line comprises a single nucleotide polymorphism (SNP) at position 2490326 of chromosome 12 of its genome, wherein the SNP comprises a substitution of an adenine for a guanine; and cultivating the identified line of smut-resistant peanuts in the geographic region. “Cultivating” is herein interpreted as being synonymous with “growing,” as is commonly understood in the art. No special definition was provided in the specification.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 1, and Claims 2-5 depending therefrom, are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite a method of identifying a peanut line based on the target sequence having at least 98% identity to the reference sequence or not. This is an abstract idea falling into the mental process grouping of abstract ideas. This judicial exception is not integrated into a practical application because the additional elements do not contribute meaningful limitation to the abstract idea.
Regarding Claim 1, the additional limitations recite obtaining a biological sample and performing whole genome sequencing on at least a portion of said sample. These are both routine processes and known in the art. The instant specification additionally states that other methodology for analyzing a large number of nucleic acids in a single reaction can be utilized, such as next generation sequencing and certain multiplex PCR-based platforms, which are also well known in the art. Regarding Claim 2, the identification step would remain the same, the target sequence having 100% identity with the reference, which would not limit the mental process. Regarding Claim 3 and 4, the SNP detected in the biological sample at position 2490326 of chromosome 12 of the target sequence comprising a substitution of an adenine for a guanine would be an inherent property of a smut-resistant allele in the biological sample, according to the rationale of the claim 7 rejection. Regarding Claim 5, Thecaphora frezzi is a known basidiomycete pathogen that has been characterized to predominantly cause peanut smut, which would not limit the abstract idea (Ospina-Maldonado, 2022).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because, when considered in combination, they do not add to the inventive concept and are generally well-understood, routine and conventional in plant science.
Regarding claim 6, Examiner notes that the recitation of recombinant inbred lines in claim 6 requires deliberate crossing of parent strains as Applicant states in the specification [¶31], thus adding a meaningful limitation and overcoming the 35 U.S.C. 101 rejection.
Claim 12, and claims 13-15 depending therefrom, are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite a method of treating or preventing peanut smut infestation by identifying a line of resistant peanuts. This is an abstract idea falling into the mental process grouping of abstract ideas of identifying if the peanut line is resistant if least one peanut from the line comprises a SNP at a specific location or if it does not. This judicial exception is not integrated into a practical application because the additional elements do not add meaningful limitation to the abstract idea.
The limitations of claim 12 state identifying a line of resistant peanuts wherein positive identification of resistance comprises at least one peanut from the line having a SNP at position 2490326 of chromosome 12 of its genome and that SNP comprising a substitution of an adenine for a guanine. As rejected in claim 7, the SNP detected in the biological sample at position 2490326 of chromosome 12 of the target sequence comprising a substitution of an adenine for a guanine would be an inherent property of a smut-resistant allele in the biological sample if the identification method as claimed were to be correct. Cultivating the identified line does not add meaningful limitation as cultivation/growing of the smut resistant peanuts could be done by one of ordinary skill in the art according to conventional methodologies.
Regarding claim 13, obtaining a line of plants from a recombinant inbred line is relatively routine in the art and has been done in peanuts (de Blas, 2021), thus not adding meaningful limitation.
Regarding claim 14, as in the rejection of claim 5 above, Thecaphora frezzi is a known basidiomycete pathogen that has been characterized to predominantly cause peanut smut, which would not limit the abstract idea (Ospina-Maldonado, 2022).
Regarding claim 15, growing the identified line of smut resistant peanuts under plant growth conditions could mean any plant growth conditions and would not add meaningful limitation.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they are considered inherent to the properties of the resistant allele and the methods are routine and conventional in the art.
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 3-4, 7-11, and 12-15 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.
In claims 3-4, the recitation of, “a single nucleotide polymorphism (SNP) is detected in the biological sample at position 2490326 of chromosome 12 of the target sequence,” seems to indicate that this SNP can be found at that position within the target sequence that has at least 98% identity to the reference sequence SEQ ID NO. 4, which is 380 nucleotides long. Claims 7-11 recite that the SNP at position 2490326 of chromosome 12 at position 2490326 of chromosome 12 is within the “resistance allele” of a crossed plant while claims 12-15 recite that one peanut from a line of smut resistant peanuts comprises the SNP at position 2490326 of chromosome 12.
The specification gives no structural characteristics allowing one of ordinary skill to locate said SNP, such as a specific line in a genome or other indicator, and it is not known to prior art. Is the SNP found within a specific target sequence? It is locatable at a specific position in any peanut genome? Additionally, based on the Peanut Base source provided by the Applicant, there are several versions of the Arachis hypogaea genome which may not have the same fixed position for the recited SNP. One of ordinary skill in the art would not be able to reliably locate this mutation based on the information provided. As such it is unclear what the Applicant is claiming and the SNP is improperly incorporated by reference.
The Examiner notes that defining the version of the reference sequence from a database with said SNP at the referenced chromosomal position at the time of filing or by giving a position relative to the SEQ ID NOs provided (i.e., SEQ ID NO. 1 or 4) with more specificity might help to overcome this rejection.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement
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.
Claim 1, and claims 5, and 6 depending therefrom, 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 positively identifying a biological target sample for peanut smut resistance with 100% identity to SEQ ID NO. 4, does not reasonably provide enablement for confirming resistance with 98% identity.
Claim 1 recites a method of identifying a peanut line that is resistant to peanut smut comprising identifying the peanut line as resistant if at least one target sequence from a biological sample comprises at least 98% identity to the peanut reference sequence SEQ ID NO. 4. The specification discloses that the gene variant that confers resistance to peanut smut in a peanut plant is located at position 2490326 of chromosome 12 of the peanut genome and that this SNP is within SEQ ID NO. 1 in Figure 1. Table 1 shows SEQ ID NO. 4 as the exemplary gene variant for peanut smut resistance with the resistance allele adenine in place of a guanine. 98% identity to SEQ ID NO. 4 would allow for 7-8 mismatches between the biological sample target sequence to the 380-nucleotide long reference sequence, said mismatches potentially including that of the SNP claimed to confer resistance. No other SNPs or biological markers are provided suggesting they could confer resistance.
To ensure that the target sequence has the mutation to the resistance allele adenine as opposed to the wild type allele guanine, the target sequence would need to have 100% identity to the reference sequence (as in claim 2) or recite with particularity that the SNP is present in the target sequence (as in claims 3 and 4) to be used in a method claim for positively identifying resistance to peanut smut.
Undue experimentation would be necessary to confirm that the 98% identity match of the target sequence to the reference sequence is indeed resistant to peanut smut.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 7-15 are rejected under 35 U.S.C. 103 as being unpatentable over de Blas et al. (2021). “Genetic mapping and QTL analysis for peanut smut resistance.” BMC Plant Biology. 21:312., as in Claims 1, 2, and 5-6 above, and further in view of Chamberlin, K., et al. (June, 2022). "Identification of Germplasm Resistant to Peanut Smut." Peanut Science. 67(9987-0987): 1-16.
This rejection is made to the extent that claims 7-15 do not recite SEQ ID NO. 4, which was not found in prior art; cf. claims 1-6, which are not rejected.
Claim 7 recites a method of producing a smut resistant peanut plant or a part thereof, comprising: crossing a peanut plant having a resistance allele associated with smut resistance with itself or a second peanut plant, wherein the resistance allele comprises a single nucleotide polymorphism (SNP) at position 2490326 of chromosome 12 and the SNP comprises a substitution of an adenine for a guanine; harvesting a resulting peanut seed; and growing the peanut seed to produce the smut resistant peanut plant or part thereof.
Claim 8 recites the method of claim 7, wherein the peanut plant is obtained from a recombinant inbred line of peanuts.
Claim 9 recites the method of claim 7, wherein the smut resistant peanut plant is resistant to peanut smut caused by colonization of Thecaphora frezzii.
Claim 10 recites the method of claim 7, further comprising employing the smut resistant peanut plant as a source of breeding material.
Claim 11 recites smut-resistant peanut plant or part thereof produced according to the method of claim 7.
Claim 12 recites a method of treating or preventing peanut smut infestation in a geographic region in need thereof, comprising: identifying a line of smut resistant peanuts, wherein at least one peanut from the line comprises a single nucleotide polymorphism (SNP) at position 2490326 of chromosome 12 of its genome, wherein the SNP comprises a substitution of an adenine for a guanine; and cultivating the identified line of smut-resistant peanuts in the geographic region.
Claim 13 recites the method of claim 12, wherein the line is obtained from a recombinant inbred line of peanuts.
Claim 14 recites the method of claim 12, wherein the identified line of smut-resistant peanuts is resistant to peanut smut caused by colonization of Thecaphora frezzii.
Claim 15 recites method of claim 12, wherein the cultivating step further comprises growing the identified line of smut-resistant peanuts under plant growth conditions.
De Blas teaches identification of peanut smut resistance caused by Thecaphora frezzi by identifying genome regions conferring smut resistance within a tetraploid genetic background. The study evaluated a RIL mapping population between A. hypogaea and a synthetic amphidiploid [(A. correntina × A. cardenasii) × A. batizocoi]4× for construction of the genetic map and a QTL analysis.
The RIL population was phenotyped for resistance to smut to show the high heritability of the resistance (pg. 6, col. 2, ¶ 2). Total genomic DNA was extracted from tissue, assayed, and analyzed to reveal SNP markers specific to each of the three parental species for construction of the genetic map (ie. Obtaining a biological sample from at least one peanut in the peanut line, performing whole genome sequencing, and generating at least one target sequence). The physical positions were designated according to the reference sequence of A. hypogaea cv. Tifrunner. Resistance genes (R-genes) were retrieved using the Intermine online platform. Gene expression for each of the gene models detected within QTLs intervals was assessed based on the A. hypogaea cv. Tifrunner reference transcriptome (Materials and Methods). Both QTLs were located within disease-resistance hotspots containing several R-genes and were suggested to be applicable for development of reliable markers for Genomics-Assisted Breeding of new varieties resistant to peanut smut, which could be done by any means known in the art (pg. 10, col. 2, ¶3). Thus, de Blas teaches a line obtained from a recombinant inbred line of peanuts, resistance to peanut smut by colonization of Thecaphora frezzi, and a smut resistant peanut plant or part thereof produced.
De Blas does not teach a SNP at position 2490326 of chromosome 12 of its genome, wherein the SNP comprises a substitution of an adenine for a guanine.
Chamberlin et al. teaches evaluation of 208 peanut genotypes for resistance to T. frezzi and identified the smut-resistant parent used in the instant application, Ascasubi, as one of the entries that appeared resistant to smut (pg. 14, col. 2, ¶ 1). Chamberlin suggests that the resistance existing in these cultivars could be suitable for incorporation into cultivars for commercial production and further states that RIL populations for mapping molecular markers associated with peanut smut resistance have been developed for use in screening of populations and in peanut breeding programs.
Examiner notes that Chamberlin has a common author with the instant application. Based on the earlier publication date of the reference (June, 2022), it constitutes prior art.
It would have been prima facie obvious to one of ordinary skill in the art to utilize the methods of de Blas with the smut-resistant parent that Chamberlin suggested was a suitable candidate for creation of RIL populations, mapping of molecular markers, and use in breeding programs. One of ordinary skill in the art would have been motivated to do so as both de Blas and Chamberlin teach the applicability of developed markers in breeding. One would additionally have reasonable expectation of success given the Ascasubi cultivar’s display of smut resistance in Chamberlin and the success in identifying prevalent QTLs in de Blas. Based on the methods and the selected cultivar, the resistance allele would inherently comprise a SNP at position 2490326 of chromosome 12, comprising a substitution of an adenine for a guanine as this mutation is conferring resistance. It would be obvious to cultivate the identified line use breeding methods such as crossing a peanut plant having a resistance allele associated with smut resistance with itself or a second peanut plant as this is a method well known in the art, as stated in Chamberlin (pg. 15, col. 1, ¶ 1).
Subject Matter Free of Art
A peanut reference sequence comprising SEQ ID NO. 4 appears to be free of prior art. The prior art fails to suggest such specifically claimed products, hence, said products are also non-obvious. Thus, claims 1-6 have subject matter free of prior art.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY K. JOHNSON whose telephone number is (571)272-5761. The examiner can normally be reached Monday - Friday 7:30 am - 5:00 pm.
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/EMILY K JOHNSON/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662