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 .
This is a Final Office Action in response to amendment filed on 7/14/2026.
Claim Status
Claims 1-2, and 9-19 are pending. Claims 1, and 2 are currently amended. Claims 3-8 are currently canceled. Claims 9-19 are newly added. Claims 1-2, and 9-19 are examined on the merits.
Response to Amendment
The rejection of Claim 1 rejected under 35 U.S.C. 101 is maintained and revised in view of the amendment. The rejection of Claims 7-8 rejected under 35 U.S.C. 101 is withdrawn in view of the cancellation of claim 7-8.
The rejection of Claims 5- 8 rejected under 35 U.S.C. 112(b) is withdrawn in view of the cancellation of claim 5-8.
The rejection of Claims 1- 8 rejected under 35 U.S.C. 112(a) is withdrawn in view of the amendments to claims 1 and 2, and cancellation of claim 3-8.
The rejection of Claim 1 rejected under 35 USC § 102(a)(1) is withdrawn in view of amendment to the claims. However, claim 1 is now rejected under 35 U.S.C. §103 for the reasons set forth below.
The rejection of claim 2 rejected under 35 U.S.C. §103 is maintained and revised in view of the amendment.
The rejection of claims 3-8 rejected under 35 U.S.C. §103 is withdrawn in view of the cancellation.
Claim Objections
Claim 2 is objected to because of informalities in the claim language, including the repeated phrase “A method of producing”. Appropriate correction 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.
Claim 1 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The claim 1 recites a correlation between the presence of the claimed polymorphism and the genotype of a soybean plant. Although claim 1 now further recites selecting a soybean plant based on the detected polymorphism and using the selected plant in a soybean breeding program, these additional limitations do not integrate the judicial exception into a practical application. Under the broadest reasonable interpretation, “using” the selected plant in a soybean breeding program does not require any specific breeding operation, such as crossing, backcrossing, producing progeny, or selecting progeny, and therefore merely applies the detected genetic information in a generic manner.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements, including nucleic acid obtaining, marker detection, PCR-based detection, sequencing, oligonucleotide probe analysis, selection of a soybean plant, and use of the selected plant in a soybean breeding program, are well-understood, routine, and conventional activities in the field and are applied in a generic manner to detect the recited polymorphisms. The recited “using” limitation does not require any particular breeding technique or technological implementation and therefore does not add significantly more than the judicial exception itself.
The instantly pending claim is method claim. The judicial exception is an abstract idea, namely a mental process, including the correlation between a recited polymorphism locus (including polymorphisms corresponding to SEQ ID NO: 1-3) and the presence or absence of peroxidase activity in a soybean plant.
Claim 1 is drawn to methods of determining the genotype of a soybean plant, which apply this correlation by detecting one or more polymorphisms and determining whether the plant has the genotype associated with the presence or absence of peroxidase activity. This claim reads on mental processes, i. e., evaluating genotype information and selecting or characterizing the plant based on that information, which amounts to observation evaluation and judgement. Although the claim additionally recites selecting a soybean plant and using the selected plant in a soybean breeding program, the claim does not require any concrete breeding step, such as crossing the selected plant with another soybean plant, producing progeny, backcrossing, or selecting progeny. Under the broadest reasonable interpretation, the “using” limitation encompasses merely employing the selected plant within a breeding program, including as breeding material or a reference, and therefore does not meaningfully limit the judicial exception.
As the steps of “obtaining a sample of nucleic acids” and “detecting” in claim 1 is very generally recited, the combination of these steps is reasonably interpreted as merely data gathering and analysis. Obtaining nucleic acids from a soybean plant and detecting polymorphisms using PCR, sequencing, probes, or other recited methods was well understood, routine, and conventional at the time of filing. There are no limitations in the claims that distinguish these steps from what is already routinely practiced. Furthermore, limiting the polymorphism to polymorphisms corresponding to SEQ ID NO: 1-3 does not change the steps to be performed. Detecting polymorphisms in plant genomic DNA and correlating such polymorphisms with a trait was routine as the time of filing.
For a claim direct to a judicial exception to be patent eligible, the claim must include additional elements sufficient to integrate the exception into a practical application and to significantly more the exception itself, as set forth in MPEP § 2106 and MPEP § 2106.04(d). Here, the additional limitations of obtaining a sample of nucleic acids and detecting polymorphisms together with selecting a soybean plant and using the selected plant in a soybean breeding program are recited genetically and merely gather, analyze, and apply information about a naturally occurring genotype-phenotype correlation using routine and conventual techniques. Because the claim does not require any specific breeding operation, such as crossing with another soybean plant or producing progeny, the recited “using” limitation does not integrate the judicial exception into a practical application and does not amount to significantly more than the judicial exception itself.
Response to Applicant’s Remarks:
Applicant argues that amended claim 1 is no longer directed merely to observing a natural correlation because the claim now recites selecting a soybean plant based on the detected polymorphism and using the selected plant in a soybean breeding program, thereby integrating the judicial exception into a practical application.
Applicant’s arguments have been fully considered but are not persuasive. Under the broadest reasonable interpretation, the recited “using” limitation does not require any specific breeding operation, such as crossing or producing progeny, and therefore does not integrate the judicial exception into a practical application or amount to significantly more than the judicial exception. Accordingly, the rejection under 35 U.S.C. § 101 is maintained.
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 1-2, 9-10, and 13-19 are rejected under 35 U.S.C. §103 as being unpatentable over Gizem (1997) in view of Rosso (M Luciana Rosso et. a., International Journal of Molecular Sciences (2021) 6;22(5):2675 pp1-16).
Claim 1 recites a method of determining the genotype of a soybean plant; comprising: obtaining a sample of nucleic acids from a soybean plant; detecting (i) the SNP position 151 of SEQ ID NO:1; or (ii) the insertion/deletion polymorphism represented by SEQ ID NO:2 and SEQ ID NO:3; and; selecting the soybean plant based on the detected polymorphism and using the selected plant in a soybean breeding program.
Gizem teaches a method of determining the genotype of a soybean plant by obtaining soybean nucleic acid and detecting a polymorphism in the soybean seed coat peroxidase locus. Specifically, Gizem teaches isolation of soybean genomic DNA, PCR amplification using primers derived from the soybean seed coat peroxidase sequence, and detection of polymorphisms that distinguish EpEp and epep genotypes (page 994, left column paragraph 1-2). Gizem further teaches that the recessive ep allele contains an 87 bp deletion at the 5’end of the structural gene, encompassing the translation start codon, and that this polymorphism co-segregates with seed coat peroxidase activity (page 994. Left column and right column).
Gizem also teaches the soybean seed coat peroxidase cDNA sequence in Figure 1 (page 992) and the 87 bp deletion in the ep allele in Figure 4 (page 993) (only a portion of the 17kb genomic sequence is disclosed). As shown by the alignment of record, SEQ ID NO: 2 matches the prior-art soybean peroxidase sequence over the aligned region, and the claimed 87 bp deletion corresponds exactly to the 87 bp deletion disclosed by Gizem in the ep allele (alignment below). Thus, Gizem teaches obtaining a sample of nucleic acids from a soybean plant and detecting in the nucleic acids the claimed insertion/deletion polymorphism.
Gizem does not expressly teach selecting the soybean plant based on the detected polymorphism and using the selected plant in a soybean breeding program.
Rosso teaches the use of molecular markers for marker-assisted selection in soybean breeding programs, including selecting soybean plants based on detected molecular markers for use in crossing and cultivar development (p1, Abstract; p11, pa1-3; p12, pa 2-5; Table8).
It would have been obvious to one of the ordinary skill in the art to use the known peroxidase-associated polymorphism taught by Gizem to select soybean plants for use in a soybean breeding program as taught by Rosso because Rosso teaches that molecular markers associated with desirable traits are routinely used to select breeding materials. One of ordinary skill in the art would have had a reasonable expectation of success because Gizem established the association between the detected polymorphism and seed coat peroxidase activity, while Rosso teaches applying such molecular markers in conventional soybean breeding.
Accordingly, Claim 1 would have been obvious over Gizem in view of Rosso.
Claim 2 recites a method of producing a soybean plant having a selected seed coat peroxidase phenotype, Obtaining nucleic acids from a soybean plant; b. Detecting; (i) a SNP at position 151 of SEQ ID NO:1, wherein the SNP comprises an A or G nucleotide: and/or (ii) the presence or absence of the 87 base pair sequence of SEQ ID NO:4 represented by SEQ ID NO:2 and SEQ ID NO:3. c. Selecting the soybean plant based on the detected genotype. d. Crossing the selected soybean plant with a second soybean plant. e. Producing progeny seed, and f. Selecting a progeny plant comprising the detected genotype.
For the same reasons set forth above with respect to claim 1, Gizem teaches obtaining soybean nucleic acids and detecting the claimed 87-base-pair insertion/deletion polymorphism associated with seed coat peroxidase activity.
Gizem does not expressly teach selecting a soybean plant based on the detected genotype, crossing the selected plant with a second soybean plant, producing progeny seed, and selecting progeny comprising the detected genotype.
Rosso teaches the use of soybean molecular markers linked to a trait in marker-assisted selection, including genotyping soybean breeding populations and selecting plants based on marker information for use in breeding programs(page 1, Abstract; page 12, paragraph 2-5; page 13, paragraph 1 and table 8; page 11, paragraph 1-3).
It would have been obvious to one of ordinary skill in the art to use the polymorphism at the known soybean Ep locus taught by Gizem in marker-assisted breeding method as taught by Rosso, including selecting plants based on the detected marker, crossing elected plants, producing seed, and selecting progeny having the desired marker and corresponding phenotype, because Rosso teaches that soybean breeders routinely use molecular markers to guide selection in breeding populations. One of ordinary skill in the art would have had a reasonable expectation of success because Gizem establishes the correlation between the polymorphism and the peroxidase phenotype, and Rosso teaches routine application of such markers in soybean breeding.
Accordingly, claim 2 would have been obvious over Gizem in view of Rosso.
Claim 9 recites the method of claim 2, wherein the selected soybean plant lacks seed coat peroxidase activity.
For the same reasons set forth above with respect to claim 2, Gizem teaches the 87-base-pair deletion associated with the recessive ep allele and reduced seed-coat peroxidase expression and activity. Gizem further teaches that the deletion removes the translation initiation codon and amino-terminal signal sequence, thereby preventing peroxidase production and accumulation of the seed-coat peroxidase. Accordingly, it would have been obvious to select an ep soybean plant lacking seed-coat peroxidase activity using the marker-assisted breeding method taught by Rosso.
Accordingly, claim 9 would have been obvious over Gizem in view of Rosso.
Claim 10 recites the method of claim 2, wherein the selected soybean plant produces seed having reduced guaiacol staining relative to a soybean plant lacking the polymorphism.
For the same reasons set forth above with respect to claim 2, Gizem teaches that soybean plants comprising the ep deletion exhibit reduced seed-coat peroxidase activity and further teaches measuring seed-doat peroxidase activity using a guaiacol staining assay (p998, left column, pa1). Accordingly, claim 9 is obvious over Gizem in view of Rosso.
Claim 13 recites the method of claim 2, wherein the selected soybean plant is advanced in a breeding program without determining seed coat peroxidase activity phenotypically.
For the same reasons set forth above with respect to claim 2, Rosso teaches marker-assisted selection in soybean breeding, whereby plants are selected and advanced based on detected genetic markers associated with a desired trait. It would have been obvious to advance a soybean plant selected using Gizem’s peroxidase-associated polymorphism without separately determining seed-coat peroxidase activity phenotypically, because the purpose of marker-assisted selection is to permit selection based on genotype. Accordingly, claim 13 is obvious over Gizem in view of Rosso.
Claim 14 recites the method of claim 2, further comprising crossing the selected soybean plant with a second soybean plant and backcrossing at least one progeny plant to a recurrent parent.
For the same reasons set forth above with respect to claim 2, Rosso teaches that the validated KASPR assay has practical applications in marker-assisted selection backcrossing and advancing breeding lines (p11, pa1). It would have been obvious to use the peroxidase-associated polymorphism taught by Gizem in such a marker-assisted backcrossing program, including backcrossing progeny to a recurrent parent, in order to introgress and retain the desired peroxidase-associated allele in a selected soybean genetic background. Accordingly, claim 14 is obvious over Gizem in view of Rosso.
Claim 15 recites the method of claim 14, wherein the polymorphism is detected in at least one backcross generation.
For the same reasons set forth above with respect to claim 14, Rosso teaches use of a KASP marker assay in marker-assisted backcrossing. It would have been obvious to detect the polymorphism in at least one backcross generation because marker-assisted backcrossing requires genotyping progeny during one or more backcross generations to identify and select plants carrying the desired marker for further backcrossing. Accordingly, claim 15 is obvious over Gizem in view of Rosso.
Claim 16 recites the method of claim 2, further comprising self-pollinating the selected soybean plant to produce at least one selfed progeny generation.
For the same reasons set forth above with respect to claim 2, Gizem teaches self-pollinating soybean plants from an EpEp x epep population to produce a selfed progeny generation and collecting progeny seed (Fig 6). It would have obvious to self-pollinate the soybean plant selected according to the marker-assisted breeding method of Gizem and Rosso to produce at least one selfed progeny generation. Accordingly, claim 16 is obvious over Gizem in view of Rosso.
Claim 17 recites the method of claim 2, wherein the polymorphism comprises the presence of the 87 base pair insertion sequence of SEQ ID NO:4. Claim 18 recites the method of claim 2, wherein the polymorphism comprises the absence of the 87 base pair insertion sequence of SEQ ID NO:4. Claim 19 recites the method of claim 2, wherein detecting the polymorphism comprises a Kompetitive Allele Specific PCR (KASP) assay or amplification of a genomic region comprising the polymorphism using polymerase chain reaction (PCR).
For the same reasons set forth above with respect to claim 2, Gizem further teaches the presence and absence of the 87-base-pair sequence in the Ep and ep alleles, respectively, and detecting the insertion/deletion polymorphism by PCR amplification of the genomic region (Fig 5 and 6).
Accordingly, claims 17-19 is obvious over Gizem in view of Rosso.
PNG
media_image1.png
902
542
media_image1.png
Greyscale
PNG
media_image2.png
427
551
media_image2.png
Greyscale
PNG
media_image3.png
779
1641
media_image3.png
Greyscale
Response to Applicant’s Remarks:
Applicant’s arguments regarding amended claim 2 have been considered but are not persuasive. Claim 2 recites detecting the SNP and/or the 87-base-pair insertion/deletion polymorphism and therefore encompasses an embodiment in which only the 87-base-paire polymorphism is detected. Gizem teaches that polymorphism and its association with seed-coat peroxidase activity, while Rosso teaches marker-assisted soybean breeding. Accordingly, the rejection of claim 2 under 103 is maintained.
Conclusion
No claims are allowed.
Claims 1-2, 9-10, and 13-19 are rejected.
Claims 11-12 are objected to as being dependent upon rejected base claims.
The closest prior art of record, Gizem, is directed to the soybean seed-coat peroxidase Ep locus and teaches an 87-base-pair insertion/deletion polymorphism associated with seed-coat peroxidase activity, including PCR-based detection of that polymorphism. However, Gizem does not teach or suggest the SNP at position 151 of SEQ ID NO:1.
In particular, claims 11 and 12 require detecting both the SNP at position 151 of SEQ ID NO:1 and the 87-base-parie insertion/deletion polymorphism, with claim 12 further requiring selection based on detection of both polymorphisms. Gizem does not disclose the specific SNP at position 151, detection of both claimed polymorphisms, or selection based on the combined marker set.
Accordingly, the prior art of record does not anticipate or render obvious the additional limitations of claims 11 and 12.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad A Abraham can be reached at (571)272-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
Prosecution Insights