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 .
Election/Restrictions
1. Applicant’s election without traverse of Group I (claims 1, 2-7 (part), 9, 10, 12 (part), 14 (part), 15 (part), 16 (part), 17 (part) and SEQ ID NOs: 1, 68, 70 (from Table 4) and 140 in the reply filed on December 5, 2025 is acknowledged.
Claims 1-42 are pending. Claims 8, 11, 13 and 18-42 are directed to non-elected subject matter are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions, there being no allowable generic or linking claim. All SEQ ID NOs. and sequences in Tables 4 and 5, except SEQ ID NO: 1, SEQ ID NO: 68, SEQ ID NO: 70 (position identifier 54 from Table 4) and SEQ ID NO: 140 are also withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions. Claims 5, 8, 16 and 17 are directed to non-elected subject matter are also withdrawn from further consideration pursuant to 37 CFR 1.142(b). It is also noted claims 7 is directed to non-elected subject matter Table 5 is also withdrawn from further consideration pursuant to 37 CFR 1.142(b).
Accordingly, Claims 1-4, 6, 9, 10, 12, 14 and 15 are examined on merits in this Office action. This restriction is made FINAL.
Applicant is reminded that upon the cancellation of claims to a non-elected invention, the inventorship must be amended in compliance with 37 CFR 1.48(b) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. Any amendment of inventorship must be accompanied by a request under 37 CFR 1.48(b) and by the fee required under 37 CFR 1.17(i).
Information Disclosure Statement
2. Initialed and dated copy of Applicant’s IDS form 1449 filed 02/09/2024 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 of the following informalities:
3. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See for example, Page 44, line 28; page 88, line 29; page 64, line 2. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01.
Appropriate action/corrections are required.
Claim Objections
4. Claims 3, 4, 6, 12, 14 and 15 are objected to because of the following informalities:
Claim 3 is objected for having non-elected subject matter “molecular marker alleles of Table 4 or Table 5”. The elected molecular allele (SEQ ID NO: 70) is from Table 4.
Claim 4 is objected for having non-elected subject matter of SEQ ID NOs: 2, 5, 6, 9, 10, 13 and 14.
Claim 6 is objected for having non-elected subject matter of SEQ ID NOs: 2, 5, 6, 9, 10, 13 and 14.
Claim 12 is objected for having non-elected subject matter of Table 4 (except SEQ ID NO: 70), and Table 5.
Claim 14 is objected for having non-elected subject matter of SEQ ID NOs: 5, 9 and 13.
Claim 15 is objected for having non-elected subject matter of SEQ ID NOs: 2, 5, 6, 9, 10, 13 and 14.
Appropriate action is required.
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.
5. Claims 1-4, 6, 9, 10, 12, 14 and 15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Analysis of claims: These claims are analyzed for eligibility in accordance with their broadest reasonable interpretation. Claim 1 recites: “A method for identifying a maize plant or plant part, comprising screening for the presence of a haplotype associated with a cytoplasmic male sterility fertility restorer locus on chromosome 3 RF-03-01.”
Step 1: To Determine whether the claim is directed to a judicial exception. The answer to this question is YES for the following reasons: The claim is directed to a natural phenomenon, namely the naturally occurring association between a haplotype and a cytoplasmic male sterility fertility restorer locus on chromosome 3 in maize plants. The claimed haplotype and fertility restorer locus exist in nature, and the association between them is a product of natural genetic inheritance. See for example, Wise et al. (TAG, 88:785-795, 1994; see in particular, abstract at lines 15-20) who mapped the fertility restorer locus (Rf1) to chromosome 3 and expressly taught that flanking molecular markers were used to identify different Rf1 alleles in segregating maize populations. Furthermore, consistent with this, Wise et al. (Genetics 143:1383–1394, 1996; see in particular, abstract at lines 5-13) subsequently demonstrated that molecularly identifiable rf1 alleles traced to naturally occurring maize inbred lines IA153 and Ky21, confirming that the Rf1 allele and associated molecular signatures existed in maize prior to any claimed screening method. This implies that the claimed haplotype is a naturally existing genetic feature of maize, and that the claim recites detection of a naturally occurring condition rather than creation of a synthetic genetic construct.
The step of “screening for the presence of a haplotype” merely observes or detects this natural correlation. Accordingly, the claim is directed to a judicial exception under Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66 (2012), as well as Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015), which hold that claims that observe naturally occurring correlations are directed to laws of nature or natural phenomena.
Step 2: To Determine whether the claim recites additional elements that integrate the judicial exception into a practical application. The answer to this question is also YES for the following reasons: The claim does not include additional elements sufficient to integrate the judicial exception into a practical application. The step of “screening” is described at a high level of generality and does not recite, for example but not limited to, a specific assay or laboratory technique, a particular molecular marker or primer set, a physical transformation of the maize plant or plant part, an improvement to a technological process, or a concrete downstream action such as breeding, producing seed, or creating a fertile plant. Therefore, the claim merely instructs one of ordinary skill in art to apply routine and conventional genetic screening techniques to observe a naturally occurring association. The use of generic screening techniques, even if well-understood, routine, and conventional, does not amount to an inventive concept sufficient to confer patent eligibility (Mayo, 566 U.S. at 79–80).
Likewise the steps of “discriminating” (claim 9) or “identification “of said haplotype in maize plant or plant part (claim 10) merely observes or detects this natural correlation, implying thereby that claims 9 and 10 too are directed to a natural phenomenon, namely the naturally occurring association between a haplotype and a cytoplasmic male sterility fertility restorer locus on chromosome 3 in maize plants (see step 1 analysis above). Likewise, claims 9 and 10 too do not include additional elements sufficient to integrate the judicial exception into a practical application as discussed above. Therefore, in the absence of such additional elements and thus use of generic discriminating or identification techniques, even if well-understood, routine, and conventional, does not amount to an inventive concept sufficient to confer patent eligibility (see step 2 analysis above).
Regarding nucleic acid sequences (markers) present between SEQ ID NO: 68 and SEQ ID NO: 140 (claim 2), elected SEQ ID NO: 70 (claim 3), elected polynucleic acid sequence as set forth in SEQ ID NO: 1 (claim 4, 6, 14 and 15) would be obviously present naturally within a naturally occurring a cytoplasmic male sterility fertility restorer locus on chromosome 3 in maize plants as discussed above. Therefore, (i) it will hold that these claims that comprises naturally occurring sequences within a plant genome as directed to laws of nature or natural phenomena (step 1), and the use of generic screening techniques, even if well-understood, routine, and conventional to identify these markers, does not amount to an inventive concept sufficient to confer patent eligibility (step 2) as discussed above.
Summary: As the claims are (i) directed to a natural phenomenon (a naturally occurring genetic association), and (ii) does not recite additional elements that amount to significantly more than the judicial exception, these claim do not meet the requirements of patent-eligible subject matter under 35 U.S.C. § 101. This is not patent-eligible pursuant to the Supreme Court decision in Association for Myriad: Assoc. for Molecular Pathology v. Myriad Genetics, Inc. (2013), Alice Corp.: Alice Corp. Pty. Ltd. v. CLS Bank Int’l (2014), Mayo: Mayo Collaborative Services v. Prometheus Labs. Inc. (2012) and Bilski: Bilski v. Kappos (2010).
It is therefore concluded that instantly claimed method does not constitute patentable subject matter.
Suggestions: To overcome this rejection, the claims may be amended to recite additional elements that integrate the judicial exception into a practical application, such as but not limited to: specific molecular detection techniques of defined genetic markers, and a concrete application of the identification step to a breeding, selection, or plant production process.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
6. Claims 1, 9 and 10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wise et al. (Theor. Appl. Genet. 88:785-795, 1994).
Regarding claim 1, Wise et al. expressly disclose every element of instantly claimed method Claim 1. Wise et al. identify rf1, a nuclear fertility restorer gene that restores male fertility to T-cytoplasm CMS maize (see abstract) Wise maps rf1 to chromosome 3 using RFLP markers (pp. 785, 787–789, Figures 1 & 2). Wise et al. further describe screening segregating progeny for fertility vs. sterility by identifying the allelic state at rf1, i.e., identifying a haplotype at the fertility restorer locus (pp. 788–792). Wise et al. further teach that detecting presence or absence of rf1 haplotypes directly identifies whether the plant is a restorer (fertile) or non-restorer (sterile). Thus, Wise discloses a method for identifying maize plants via screening for haplotypes associated with the chromosome 3 restorer locus — which is exactly what Claim 1 requires.
Regarding claim 9, Wise et al. disclose discrimination between haplotypes linked to fertility restoration vs. sterility. Wise et al. explicitly distinguishes plants with the rf1 haplotype → Fertile (restorer) and plants without the rf1 haplotype → Sterile (non-restorer). At page 788, Wise et al. disclose segregation analysis which distinguishes fertile vs. sterile plants using marker haplotypes At pages 789–790 and Figure 2 Wise et al describes the restorer haplotype vs. non-restorer haplotype, and at page 792, Wise et al. teach that rf1-linked haplotype was used to identify restorer vs. non-restorer genotypes. Thus wise et al. clearly discriminates plants based on presence/absence of the chromosome 3 restorer haplotype and thus anticipates the claim 9.
Regarding claim 10, Wise et al. disclose detecting a haplotype and identifying the plant as a restorer if detected. The reference describes identification of said haplotype if the haplotype is detected. At pages 787-788, the references describes detecting specific RFLP haplotypes linked to rf1. Furthermore, at Figure 2 (page 789), the reference describes visualization of the haplotype used to determine which plants carry rf1. Likewise, at page 790, the reference describes detection of the rf1-linked marker identifies restorers, and at page 792, Wise et al. describe detection of the linked haplotype allows identification of restorer genotypes. Thus Wise et al. identifying plants as rf1-positive when the haplotype is detected. This fully anticipates Claim 10.
Thus, in summary, Wise et al. disclose all the elements of instantly claimed method comprising (i) screening for said haplotype; (ii) linking said haplotype to a chromosome 3 fertility restorer locus (rf1); (iii) detecting said haplotype using molecular markers; (iv) identifying plants as restorers if they possess the haplotype; and (iv) distinguishing restorer vs. non-restorer plants based on haplotype presence or absence.
Accordingly, Wise et al. anticipated the instantly claimed method.
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
7. Claim(s) 1-4, 6, 9, 10, 12, 14 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over to claim Wise et al. (Theor. Appl. Genet. 88:785-795, 1994) above, and further in view of Jiao et al. (Nature, 546:524-527, 2017) and NCBI/GenBank B73 RefGen_v4 assembly (NCBI RefSeq assembly: GCA_000005005.6, 2017, pages 1-8).
Wise et al. teach the genetic localization of nuclear fertility restorer loci for Texas (T) cytoplasm male sterility in maize. Specifically, Wise et al. mapped the rf1 locus on chromosome 3 based on RFLP linkage analysis in multiple mapping populations. The consensus map produced in Wise et al. places rf1 between the RFLP markers umc97 and umc92 on chromosome 3, and demonstrates that these markers co-segregate with restoration of fertility in T-cytoplasm male-sterile plants. This establishes that a fertility-restoring gene resides in a defined genetic interval on chromosome 3. See in particular, abstract; materials and methods at right column of page 786 through left column of page 789; results and discussion; Tables 1-5; Figures 1-4.
While Wise et al. identifies the chromosomal location and genetic interval of rf1 on maize chromosome 3, it does not disclose the complete nucleotide sequence of chromosome 3, nor does it provide specific DNA marker sequences corresponding to the claimed SEQ ID NOs (1, 68, 70, 140). Wise et al. teachings is limited to genetic marker names and map positions and does not supply base-pair sequence information, sequence coordinates, nor any assay, primer, probe, or contiguous genomic sequence that corresponds to the claimed molecular marker sequences.
Jiao et al. teach the improved maize reference genome assembly B73 RefGen_v4, constructed with single-molecule long reads, optical mapping, and a high-density genetic map. This reference genome provides chromosome-level pseudomolecules including full sequence for maize chromosome 3, enabling precise physical mapping of genes and markers. Jiao et al. teachings are directed to the assembly process, the metrics of contiguity, and the fact that previously fragmented regions are now contiguous at the megabase scale, which facilitates detailed sequence analysis of genetic loci of interest. See in particular, Figs. 1-3; Tables 1-2, pages 524-526. The availability of RefGen_v4 allows skilled artisans to align or place any short DNA sequence (such as the claimed Seq ID NOs: 1, 68, 70 and 140) onto a specific coordinate on chromosome 3 using routine bioinformatics tools (e.g., BLAST, BLAT). It may be noted that instant SEQ ID NO: 68 is also published as GenBank Sequence Accession No. AC211583, Published 2013; SEQ ID NO: 140 is also published as GenBank Sequence Accession No. AC207794, Published 2013; SEQ ID NO: 70 is also published as GenBank Sequence Accession No. CC352881, Published 2003 and SEQ ID NO: 1 is also published as GenBank Sequence Accession No. XM_020549870, Published 2017.
Public GenBank records associated with the B73 RefGen_v4 assembly (GCF_000005005.6) provide the full assembled nucleotide sequence of maize chromosome 3 and are accessible via NCBI’s Assembly database. These records were available in 2017, consistent with the timeline of the cited publications. Publicly available assembly of Zea mays B73 chromosome sequences Published 2017, provides publicly accessible, complete chromosome-level sequences of maize including chromosome 3 that are routinely used for sequence alignment and marker positioning. They enable routine alignment of short nucleotide sequences to reference chromosomes and permit a skilled artisan to determine whether a given sequence resides on chromosome 3 and to extract its precise base-pair coordinates. Such routine use of publicly available genomic sequences for marker localization is widely practiced and well understood in the field. As discussed above instant SEQ ID NO: 68 is also published as GenBank Sequence Accession No. AC211583, Published 2013; SEQ ID NO: 140 is also published as GenBank Sequence Accession No. AC207794, Published 2013; SEQ ID NO: 70 is also published as GenBank Sequence Accession No. CC352881, Published 2003; and SEQ ID NO: 1 is also published as GenBank Sequence Accession No. XM_020549870, Published 2017.
It would have been obvious to one of ordinary skill prior to earliest filing date of the claimed invention to combine the teachings of Wise et al. with the complete sequence information provided by Jiao et al. and the corresponding GenBank B73 RefGen_v4 assembly records as discussed above.
Given (i) Wise et al. teach that the male fertility restorer locus (rf1) for T-cytoplasm is located on chromosome 3 between known genetic markers.; (ii) the availability of a complete chromosome 3 sequence in Jiao et al. (2017); and (iii) GenBank RefGen_v4 would have obviously enabled a skilled artisan prior to earliest filing date of the claimed invention to map genetic loci to physical sequence coordinates which is a routine task in genomics. Given Wise et al.’s genetic interval on chromosome 3, a person of ordinary skill would naturally seek to leverage the complete reference to identify, align, and characterize nucleotide sequences in that region and thus provides a clear motivation to target chromosome 3 for physical sequence analysis related to fertility restoration.
It may be noted that (i) using standard bioinformatics tools such as BLAST or BLAT to align short nucleotide sequences against the publicly available B73 RefGen_v4 chromosome 3 pseudomolecule is routine and well-established in maize genomics; (ii) converting genetic map positions (Wise et al., e.g., umc97 and umc92) to physical coordinates on RefGen_v4 using reference genome browsers (e.g., Maize DB, NCBI) is a routine application of genomic resources; (iii) identifying or designing nucleotide markers in a defined physical interval once the sequence is available is a conventional step in molecular marker development, it would have been obvious and within the scope of ordinary skill in the part prior to earliest filed date of the instantly claimed invention to have combined the cited prior art to arrive at the applicant’s invention by employing routinely used predictable techniques as discussed above.
Given the state of maize genomics and the completeness of the B73 RefGen_v4 sequence, a person of ordinary skill in the art prior to earliest filing date of the instantly claimed invention would have had a reasonable expectation that aligning the claimed sequences (SEQ ID NOs 1, 68, 70, 140) to the chromosome 3 reference would locate them within or near the rf1 locus interval identified by Wise et al. The predictable use of complete genomic sequence to localize markers within a known genetic interval would have eliminated any unpredictability.
Accordingly, the claimed method of identifying or using specific molecular marker sequences on maize chromosome 3 associated with a cytoplasmic male-sterility fertility restorer locus would have been obvious under 35 U.S.C. §103 in view of Wise et al. combined with Jiao et al. and the publicly available B73 RefGen_v4 GenBank assembly records. It may be reiterated that Wise et al. provides the genetic localization of the restorer locus on chromosome 3; Jiao et al. and GenBank provide detailed sequence information enabling physical mapping of claimed sequences within that locus. Thus, routine use of these teachings would have led to the claimed subject matter with predictable results.
Thus, the claimed invention as a whole is prima facie obvious over the combined teachings of the prior art.
Conclusions
8. Claims 1-4, 6, 9, 10, 12, 14 and 15 are rejected.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to VINOD KUMAR whose telephone number is (571)272-4445. The examiner can normally be reached on 8:30 am - 5.00 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad A. Abraham can be reached on (571) 270-7058 The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/VINOD KUMAR/Primary Examiner, Art Unit 1663