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 .
Claim Status
Claims 1-2, 4 & 6-7 are under examination on the merits.
Claims 3 & 5 are cancelled.
Priority
Claims 1-2, 4 & 6-7 receive the U.S. effective filing date of 11/23/2022. Foreign priority to CN202211470272.9 is claimed and acknowledged.
Previous 112(d) rejection of claim 4 is withdrawn in view of Applicant’s claim amendment.
Previous 112(b) rejection of claims 1-2 & 4 is withdrawn in view of Applicant’s claim amendment.
Previous 102(a)(1) rejection of claim 1-2, 4 & 6-7 over Ali is withdrawn in view of Applicant’s claim amendment and arguments.
Previous 103 rejection of claim 6 is withdrawn in view of Applicant’s claim amendment.
Drawings
The drawings are objected to because Figures 6 & 10 are unreadable due to low resolution and/or the formatting of the graph(s). Figure 6 has unreadable superscripts. Figure 10 has unreadable error bars. These figures require higher resolution images and/or reformatting so as to be readable.
In general, use of a dark background will make error bars unreadable and this is why data for osrnr10-1 and osrnr10-2 (both dark bars) is unclear. Applicant is advised to increase the font size in Figure 6 to make superscripts readable, and to adjust formatting of ‘bars’ presented in Figure 10 to a lighter shade of grey so the error bars describing effects of osrnr10-1 and osrnr10-2 are legible.
Corrected drawing sheets in compliance with 37 CFR 1.121 (d) are
required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as "amended." If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency.
Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either "Replacement Sheet" or "New Sheet" pursuant to 37 CFR 1.121 (d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code [p.7, par.2]. 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.
Applicant is advised to check whether language is browser-executable code by copy/pasting into a web browser – if the URL link goes directly to a website, as opposed to pulling up general search results, then the hyperlink is browser-executable code. Gramene is a well-known genetics resource and can be cited using research publications rather than directly linking to the database.
Claim Rejections - 35 USC § 112
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 7 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 7 simply restates the method of claim 1 (i.e. a method of using OsRNR10 to optimize rice root systems, Nitrogen Use Efficiency [NUE], and yield) and does not provide any further limitation to the previously recited subject matter.
Lines 2-3 of claim 1 state the OsRNR10 gene is used to (a) optimize rice root system development and (b) improve rice nitrogen use efficiency and yield. Claim 7 recites only two limitations; using OsRNR10 to (a) optimize rice root system development and (b) improve rice nitrogen use efficiency and yield. These are the same limitations as presented in claim 1 and provide no further narrowing of the scope of the invention.
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.
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.
Due to Applicant’s amendment of the claims, the rejection is modified set forth in the Office action mailed 07-16-2025 as applied to claim 6.
Claim 6 is 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.
Independent claim 6 recites applicant’s designated ‘OsRNR10’ gene, and/or its promoter sequences. This is a descriptive term coined by the applicant that has no precedent in prior art which would unambiguously specify the genetic sequence it consists of. There is no specifically claimed SEQ ID in claim 6 which unambiguously defines the sequence OsRNR10 being claimed by applicant.
Because there is no definition of the genetic architecture or sequence of OsRNR10 in the prior art, it is particularly unclear what is being limited to in claim 6. Therefore it would be unclear to one what is actually being claimed by applicant, what the specific metes and bounds of the claim limitations are, or how one would avoid infringing such claims. Because of this, as currently written, claim 6 is rejected.
Claims 1-2 & 7 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.
Attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. 112(b) or pre-AIA I 35 U.S.C. 112, second paragraph. See MPEP 2173.05(q).
Claims 1-2 & 7 are drawn to ‘use’ of OsRNR10 to optimize or improve plants. However, the claims do not recite any active, positive steps indicating what one would do to achieve optimized or improved plants following detection of the allelic state of OsRNR10 and/or its promoter. No additional claim limitations are recited to inform the reader what the claimed use encompasses beyond agronomic ‘optimization’ or ‘improvement’ of rice.
Because they fail to set forth any steps involved in the claimed ‘use’ or process involved, claims 1-2 & 7 are rejected.
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.
Due to Applicant’s amendment of the claims, the rejection is modified set forth in the Office action mailed 07-16-2025 as applied to claims 1-2, 4 & 7. Applicant’s arguments filed 10-15-2025 have been fully considered but are not persuasive.
Claims 1-2, 4 & 7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to detection of a natural principle/phenomena without significantly more. Claims recite methods of detecting or using a naturally occurring allele, OsRNR10, based on its markers. This judicial exception is not integrated into a practical application because the claims simply recite a method of diagnosing or ‘using’ the naturally occurring allele without substantially more.
The OsRNR gene and promoter are naturally occurring in rice. Prior art demonstrates that two auxin-responsive alleles, one of which is the claimed OsRNR10, differentiate the subspecies of cultivated rice [See Zhang 2020; p.573, col.2, par.2]. Applicants’ specification provides further evidence of this, in their statement that screening of 3,000 rice accessions indicates the claimed allele clearly differentiates indica or japonica backgrounds [See Instant Application; p.13, par.2; p.14, par.2].
Rice plants in the indica subgroup of rice have low/no expression of the OsRNR10 gene which results in their generally ‘less compact’ roots and higher NUE than rice in the japonica subgroup. Japonica rice has high expression of OsRNR10 due to action of the promoter, which leads ‘more compact’ roots and lower NUE [Specification, p.3, par.4]. Claimed methods consist of detecting the allelic state OsRNR10 allele and/or its promoter and selecting these corresponding phenotypes. These are one and the same as the naturally occurring, primary differentiator of the indica subspecies of cultivated rice, its root architecture and agronomic characteristics. The presence of this functioning or null allele for OsRNR10 would be visibly detectable or diagnosable based on phenotype.
Claims 1-2 & 7 recite this general ‘use’ of OsRNR10 and/or its promoters for the beneficial phenotypic effects it confers. However, this does not differentiate the claims from the processes occurring in nature, as it simply provides a molecular diagnostic test for the naturally occurring gene, which is causative of the existing phenotypic or adaptive differences between indica and japonica rice. Therefore, these claims are not directed to significantly more than a process of nature.
Claim 4 recites the additional element of detecting OsRNR10 using molecular markers. This is presented as a ‘method for determining’ the phenotypic effect of OsRNR10 alleles. However, this does not differentiate the claim from processes occurring in nature, as this is simply drawn to diagnosis of which form of the naturally occurring gene or alleles is present in a given rice plant. Similar differentiation could reasonably be made by examination of the root architecture of a given plant. Therefore, this claim is not directed to significantly more than a process of nature.
Further, claims to such would encompass any past, current, or future breeding work utilizing crosses between these two subspecies. Any selection of rice for root architecture, NUE, or yield in common field trials would potentially detect or ‘use’ the naturally occurring alleles now being claimed by Applicant. Applicant simply diagnoses this known, existing natural genetic variation using modern genotyping technology. These are adaptive characteristics which already phenotypically differentiate particular genetic groups in rice, and known to be the result of different allelic states of OsRNR10 and/or its promoter(s).
Because this claim is directed to the detection of a naturally occurring allele (sequence) of a naturally occurring gene (OsRNR10) which clearly differentiates the two major subspecies of cultivated rice, claims 1-2, 4 & 7 are rejected.
Claims 1-2 & 7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because they attempt to claim a process without setting forth any steps involved in the process.
“Use” claims that do not purport to claim a process, machine, manufacture, or composition of matter fail to comply with 35 U.S.C. 101. See MPEP 2173.05(q).
Claims 1-2 & 7 are drawn to ‘use’ of OsRNR10 to optimize or improve plants. However, the claims do not recite any active, positive steps indicating what one would do to achieve optimized or improved plants following detection of the allelic state of OsRNR10 and/or its promoter. No additional claim limitations are recited to inform the reader what the claimed use encompasses beyond agronomic ‘optimization’ or ‘improvement’ of rice.
Because they recite a use but fail to recite steps involved in such, claims 1-2 & 7 are rejected.
Response to Arguments
Applicant traverses 101 rejection of claims as drawn to a natural phenomenon. They state such rejection is improper based on the distinction between claims which recite an exception and those which merely involve an exception. Applicant’s position is that claims drawn to use of naturally occurring allele(s) and their genetic diagnosis based on molecular markers is of the latter category. Applicant states that methods involving such naturally occurring alleles are patentable subject matter and points to Example 43 of the USPTO’s Subject Matter Eligibility Guidance describing blood assays.
However, Example 43 utilizes a step (administering) that is a practical application of the detection of the naturally occurring genetic markers. In the example, biomarkers are detected (i.e. measuring both C11 and C13), they are then used to calculate a specific ratio (i.e. calculating ratio of C11:C13), and then a method of treatment is administered (i.e. administering a treatment). The example cited uses detection of naturally occurring biomarkers as a preliminary step of identifying genetic variation that is then used in a practical application (i.e. an active step applying that information). Applicant does not present such a practical application or otherwise indicate a specific action taken with information provided by the molecular markers.
Applicant’s claims merely recite the detection of a naturally occurring allele and/or its associated promoter associated with their naturally occurring phenotypes (i.e. improved nitrogen use and/or a desired root architecture). The claims do not involve a naturally occurring allele as part of a more substantial practical application or methodology, but rather directly recite and claim the allele, its naturally occurring associated genetic sequences, and the generic diagnosis of plants carrying the gene absent further active method steps.
Because of this, Applicant’s argument is unpersuasive.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Due to Applicant’s amendment of the claims, the rejection is modified set forth in the Office action mailed 07-16-2025 as applied to claims 1-2, 4 & 7. Applicant’s arguments filed 10-15-2025 have been fully considered but are not persuasive.
Claims 1-2, 4 & 7 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang [Plant Cell. 2021 May 5;33(3):566-580; Published 12-29-2020] in view of Negrão [Molecular breeding, 2008-09, Vol.22 (2), p.159-168; Published 03-21-2008].
In 2020 Zhang disclosed two genetic loci (QTL) that regulate auxin homeostasis, determine root architecture and NUE in rice [p.570, col.1, par.3]. One of these two QTL correspond to a region encompassing the OsRNR10 allele. Their research disclosure is focused on genes involved in hormonal regulation of root development and identifies ‘DULL NITROGEN RESPONSE’ QTL on chromosome 1 (qDNR1) and chromosome 10 (qDNR10) [p.568, ‘Results’, par.1]. Both of these QTL are indicated as impacting the same phenotypic and agronomic characteristics of the instant application. While Zhang focuses their journal publication on qDNR1, they nonetheless disclose the functional allele of the instant application on chromosome 10.
They state that root architecture, NUE and yield responses are due to two loci on chromosome 10. They describe generally how these two ‘DULL NITROGEN RESPONSE’ alleles function physiologically in rice to increase NUE [p.566, ‘Abstract’] They clearly indicate the presence of two alleles controlling root architecture, NUE, and yield including the locus qDNR10, comprising the naturally occurring promoter and gene sequences corresponding to OsRNR10 claimed in the instant application. Further, they describe how loss-of-function at the DNR loci phenotypically impacts rice, and suggest practical application of such null mutants from indica germplasm. Their publication essentially describes the genetic factor influencing root architecture in the instant application (OsRNR10), as well as teaches methods directed to use in breeding an improved japonica-type rice with higher NUE, and therefore yield potential, based on alteration to root architecture.
With respect to claim 4 of the instant application, comparison of Zhang’s figure 1(b) depicting QTL location on chromosome 10 to figure 1(a) of the instant application shows a corresponding physical position between the target root architecture/NUE QTL region on chromosome 10 and applicant's claimed sequence. Zhang indicates location of their indica root-architecture QTL between markers RM147 & RM591, and the claimed sequence of the instant application is fine-mapped to between RM228 and the end of the chromosome [Figure 1a]. Comparison to rice linkage maps indicates the fine-mapped region is within the previously reported marker interval [see Figure 1b; Orjuela et al. Theor Appl Genet (2010) 120:563–572; Published 10-22-2009]. This indicates applicant's claimed sequence is simply a routine ‘fine-mapping’ description of the previously reported QTL, effecting the same functional phenotype, and that this claimed functional sequence is entirely within the bounds of and underlying the genomic region disclosed by Zhang in 2020.
Additionally, SEQ ID NO.1 & 2 are described by applicant as being a naturally occurring allele sequences present and/or differentiating the known major indica and japonica germplasm pools of cultivated rice [p.13, par.2; p.14, par.2]. This echoes Zhang’s 2020 disclosure of the two major DNR QTL in 2020, where their research indicated such alleles diverge as functional/non-functional between the two major subspecies japonica and indica [p.573, col.2, par.2]. Applicant is simply diagnosing and providing a more detailed sequence description of a naturally occurring and previously disclosed locus.
Zhang does not go on to describe the specific breeding process or use of marker-assisted selection in creating germplasm with the described indica QTL for modified root architecture, NUE, and yield.
However, this is remedied by Negrão who teaches the applied breeding usage of indica X japonica rice crosses in order to transfer desirable traits from indica to japonica-types. In their 2008 publication, they describe the well-characterized differentiation between the indica and japonica germplasm pools and active efforts to combine the best morphological characteristics of each, including root characteristics, into an optimal agronomic phenotype (ideotype) preferably in a japonica background. They state transfer of traits between the two subspecies has been an active area of research since the 1990s [p.162, col.2]. Further, they suggest use of molecular markers in conjunction with traditional phenotypic means of selection to transfer beneficial alleles from indica to other pools of rice germplasm [p.164-165, ‘Relevance of molecular tools to breeding: building a bridge’].
Broadest reasonable interpretation of claims 1-2, 4 & 7 would indicate that use of any indica rice plant in breeding with concurrent selection for yield in a fertilized agricultural system may be reasonably expected to select null OsRNR10 (indica) alleles. Because it appears the null OsRNR10 allele is almost universally present in global indica rice germplasm, or at least the 3,000 sampled accessions tested, the claims as written would potentially read on any previous, current, or future use of indica rice germplasm in rice breeding programs. Use of indica rice when selecting for yield improvement would potentially capture OsRNR10 alleles in the process due to their profound phenotypic effect, even in absence of genomic or molecular data.
The OsRNR10 loci and its phenotypic effect was previously described, as were methods of transferring its beneficial alleles and selecting for improved agronomic characteristics using indica x japonica rice crosses. Zhang directly suggests that plant breeders could manipulate such auxin-related DNR genes as, “a promising strategy for sustainably increasing grain yield” [p.573, col.1, par.2]. Negrão teaches the various methods for transferring such promising alleles in an applied breeding program.
One would clearly be motivated to combine such prior art in order to be able to increase NUE, and subsequent yield, of japonica rice or material derived from indica X japonica crosses. One would also plainly see the advantages of combining the beneficial NUE and yield characteristics of the chromosome 10 ‘DULL NITROGEN RESPONSE’ allele disclosed by Zhang in 2020 with the general teaching of applied breeding directed to indica alleles conferring beneficial traits, as outlined by in the review of Negrão. Because improvement of NUE and yield is an almost universal goal of grain breeding programs worldwide, it would be obvious and routine to seek out and use a naturally occurring, known, and previously reported QTL, or the gene comprising such a QTL, as a selection target in a breeding program.
Because of the obviousness of these claims in view of prior art, claims 1-2, 4 & 7 are rejected.
Response to Arguments
Applicant traverses 103 rejection of claims 1-2, 4 & 6 and argues that Applicant’s description is the first revelation of the ‘nitrogen-auxin co-regulation pathway’ not mentioned in any of the prior art. They argue that this fact, and specific molecular characteristics associated with OsRNR10 described in their specification, make their Application and claims novel or non-obvious.
However, the claims do not recite ‘nitrogen-auxin co-regulation pathways’, ‘novel regulatory pathways’, or ‘monoubiquitinating the K53 site of OsDNR1’ as currently argued. Claims only recite general methods of detecting or using OsRNR10 and its naturally occurring alleles in breeding for NUE and improved root architecture.
The claim language, as written, merely recites observing or detecting the natural phenotypic effects of OsRNR10 and its associated promoter(s). These are naturally occurring alleles whose genetic location and phenotypic effect was described by Zhang. Further, the methods of using such beneficial alleles in plant breeding using indica x japonica crosses is fully described by Negrão. The relationship between rice plant NUE (i.e. nitrogen use pathways) and plant architecture (i.e. auxin pathways) was clearly known in the art. Further, refined technical description of alleles already in public use is not novel or inventive per se, absent additional steps providing novel methodology (see response to 101 argument above).
As such, Applicant’s arguments are unpersuasive.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 EST.
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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Anne Kubelik/Primary Examiner, Art Unit 1663