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, 5, 7-10, 12, 14, 16, 21, 29, 32, 36-37 & 39 are under examination on the merits.
Claims 61, 69, 72, 77 & 79 are withdrawn from examination as being directed to non-elected inventive groups.
Priority
Claims 1, 5, 7-10, 12, 14, 16, 21, 29, 32, 36-37 & 39 receive the U.S. effective filing date of 04/21/2022.
Previous rejection of claims 1, 5, 8-10, 16 & 21 under 35 U.S.C. 101 is withdrawn in view of Applicant’s amendment to the claims.
Previous rejection of claims 1, 5, 8-10, 12, 14, 16 & 21 under 35 U.S.C. 102(a)(1) is withdrawn in view of Applicant’s amendment to the claims.
Previous rejection of claim 7 under 35 U.S.C. 103 over Zhang is withdrawn in view of Applicant’s amendment to the claims.
Previous rejection of claims 29, 32, 36-37 & 39 under 35 U.S.C. 103 over Zhang in view of Hou is withdrawn in view of Applicant’s amendment to the claims.
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.
Claims 1, 5, 7-10, 12, 14, 16, 21, 29, 32, 36-37 & 39 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang [Plant Biotechnol J. 17(12):2272-2285 (2019); Published 20 May 2019, with supplement] in view of Prakash [2019 Electronic Journal of Plant Breeding, 10 (2): 518-524; Published 8 Aug 2021] and Chapman [Journal of Experimental Botany, Vol. 72, No. 22 pp. 7710–7728; Published 8 Aug 2021].
The claims are drawn to generating a maize plant with the ‘staygreen’ phenotype due to presence of a mutated, non-functional NAC7 gene.
Zhang teaches the role of NAC7 in the staygreen phenotype and increased yield of maize. They disclose germplasm with a deletion mutation in the NAC7 gene as well as describing the effect of NAC7 [p.2272, ‘Summary’]. Zhang provides sequence of NAC7 as gene model GRMZM2G114850 or ‘nactf108’, submitted to the MaizeGDB database, and describes its role in the stay-green phenotype. Zhang describes the corresponding increase in yield seen in the germplasm of the Illinois Low Protein (ILP) maize population [p.2274, col.1, par.1].
Zhang teaches the role of NAC7 through traditional QTL mapping of the naturally occurring NAC7 alleles in the Illinois High/Low Protein maize populations, and functionally verifies them using ‘knock-out’ or ‘knock-down’ mutants via RNAi gene silencing.
Zhang teaches a sequence (‘nactf108’) of 94.47% identity (i.e. ‘at least 80% sequence identity’) to Applicant’s SEQ ID NO.72 [See MaizeGDB alignment in attached SEQ ID NO:72 NCBI search results]:
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Zhang teaches a sequence (‘nactf108’) of 98.42% identity (i.e. ‘at least 80% sequence identity’) to Applicant’s SEQ ID NO.75 [See MaizeGDB alignment in attached SEQ ID NO:75 NCBI search results]:
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Zhang teaches the naturally occurring NAC7 gene, as well as one of its reduced expression alleles. They clearly identify naturally occurring wild-type and mutant alleles of NAC7. These are associated with known phenotypes in the Illinois High & Low Protein maize populations [p.2272, ‘Summary’].
Zhang teaches the NAC7 gene and provides depiction of variant alleles in Supporting Figure 2. This shows insertion/deletion of 1-12 nucleotides in the Exon 2 region of the NAC7 gene (i.e., at least one mutation is a deletion of at least one base pair), which causes a truncation of the NAC7 protein (i.e., ‘a mutated NAC7 gene that produces a truncated…polypeptide’). The insertion/deletion of nucleotides as depicted by Zhang results in a frame shift and premature stop codon causative of the protein truncation, and the diminished expression producing the ‘staygreen’ phenotype known to occur in the Illionois Low Protein germplasm.
Zhang’s teaches mutation in Exon 2 results in a truncated NAC7 protein without the C-terminus end of the protein, which includes loss of at least one amino acid residue (i.e. ‘truncation of one amino acid’).
Zhang teaches NAC7’s impact on yield via increased biomass [p.2275, col.1, par.2 & Figure 3]. Zhang states that functional stay-green results in higher grain yield, and teaches that crosses involving nac7 mutants (i.e. ‘staygreen’ phenotypes) produced hybrids with increased grain yield over multiple years and environments [p.2272, ‘Summary’; p.2280, col.2, par.1].
Zhang teaches a sequence (‘nactf108’) of 93.99% identity (i.e. ‘at least 90% sequence identity’) to Applicant’s SEQ ID NO.114. [See MaizeGDB alignment in attached SEQ ID NO:114 NCBI search results]:
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Zhang does not teach the inclusion of an intact NAC domain per se. Zhang does not teach the specific mutation regions, mutations, or subcomponent/fragment sequences outside of Exon 2, and limited to by Applicant in claim 7.
Chapman teaches that NAC transcription factors can be manipulated, or mutated to have a loss-of-function and induce staygreen phenotypes via base pair substitutions (i.e. still possessing an intact NAC domain).
Chapman teaches the manipulation of NAM-1, which is a NAC gene, in wheat [p.7711, col.1, par.3]. They teach EMS mutagenesis to cause point mutations which substitute G:A and C:T transitions in NAM-1 [p.7713, col.1, par.4]. They describe mutants with intact NAC domains that result in missense mutations that negatively impact function of the expressed NAM-1 protein by interfering with higher-level protein structure [p.7716, col.2, par.2; p.7719, Table 2]. They teach that mutations within the NAC domain exhibited altered senescence (i.e. staygreen) patterns, and that such novel allelic variants with an intact NAC domain can potentially enhance yield [p.7725, col.1, ‘Conclusions’].
Thus, Chapman teaches that in addition to the known deletion mutants, base pair substitutions or alterations in the context of intact NAC domains can also lead to reduced or loss of function of encoded NAC protein, resulting in the ‘staygreen’ phenotype, replicating the functional effects taught regarding deleterious mutations but with potentially valuable, more nuanced effects on senescence phenotypes.
Before the effective filing date of the invention, it would have been obvious to one of ordinary skill in the art to modify the loss of NAC7 function taught by Zhang to alternate loss-of-function alleles of NAC7 including those with intact NAC domains via substitution or point mutations, as described in Chapman.
One of ordinary skill in the art would have been motivated to generate or utilize such a mutation because the art of Zhang teaches the disruption of nac7 in naturally occurring maize mutants leads to increased yield via staygreen [p.2272, ‘Summary’; p.2280, col.2, par.1]. Chapman teaches methods of disrupting of the nac7 ortholog in wheat via man-made mutations generating various ‘staygreen allleles’ having intact regulatory NAC domains [p.7716, col.2, par.2; p.7719, Table 2].
Replicating the natural nac7 mutant by disrupting or reducing activity of the NAC protein, while retaining the intact NAC regulatory domain (as in Chapman) would produce allele(s) with the potentially added benefit of having more varied or fine-tuned effects on senescence as well as other yield characteristics relevant to grain-filling [p.7725, col.1, ‘Conclusions’]. Chapman describes that varied allelic effects are seen when this is done in wheat, while retaining overall staygreen (i.e. increased yield) phenotype, when the NAC domain is included rather than being deleted completely from gene variants [p.7724, col.2, par.3—p.7725, col.1, par.1]. They teach that such allelic variants contribute ‘more subtle phenotypes’ that may be beneficial to refine application of staygreen alleles in breeding programs [id]. One skilled in the art of plant breeding would be motivated to cross-apply such man made nac7 mutations in corn, to test for ‘improved’ staygreen alleles differing from the natural NAC domain deletion mutant described in the Illinois High & Low selection populations.
With respect to specific location of particular mutations, claim 7 is drawn to introducing a mutation in the region downstream of Exon 2. The naturally occurring mutant features truncation (shortening) of the polypeptide at Exon 2, disrupting the protein’s function. It would be clear that disrupting the protein’s function using other mutational strategies would predictably produce a staygreen phenotypes. Such a protein would reasonably be expected to recreate the previously disclosed mutant ‘staygreen’ phenotype associated with truncation caused due to mutation at exon 2, albeit via a different form of mutation.
Regarding claims 1, 14, 21, 29, 32, 36-37 & 39 the limitation of sequence identity and inclusion of intact NAC7 domain is met by Zhang who teaches sequences which have 94.47%, 98.42%, & 93.99% similarity to those claimed by Applicant, in view of Chapman who teaches substitution mutation of intact NAC genes can generate varied alleles conditioning staygreen phenotypes.
Regarding claims 5, 7-10 & 12, the limitation(s) of specific mutations in NAC7 is met by Zhang who teaches allelic variants of NAC7 transcription factors lead to the naturally occurring staygreen phenotype, in view of Chapman. This is because Chapman teaches methods of specifically mutating such transcription factors, in a directed manner, to generate mutant alleles resulting in staygreen. Chapman teaches that mutations within the NAC region can lead to alleles with varied ‘staygreen’ phenotypes; such mutations that retain the NAC region, as alternate ‘staygreen’ alleles, may have varied or improved function over the more drastic deletion-based mutants which are absent the entire NAC domain.
Because ‘staygreen’ is a trait of known importance [Zhang, p.2272, col.1, par.2—col.2, par.1], and NAC transcription factors have complex interaction with other important physiological changes occurring during senescence and yield-formation [Chapman, p.7711, col.1, par.2], the generation of such varied alleles for further testing which comprise an overall truncated protein, but retain the NAC domain, would be of interest to a plant breeder.
A plant breeder would want the ability to assess these alternate man-made ‘staygreen’ alleles in other genetic backgrounds in the same way they would want to assess varied natural alleles for a gene of known importance. Characterizing and deploying alternate alleles with positive agronomic characteristics is the basis of applied plant breeding, and routine. Generating mutations that retained the NAC domain would only require retention of that domain within SEQ ID NO.72, and as such, alternate mutant variant alleles with as little as 80% identity to SEQ ID NO.72 could maintain the NAC domain feature taught by Chapman while generating a truncated, or otherwise mutant, non-functional protein resulting in ‘staygreen’ and increased yield.
Regarding claim 16, the limitation of increasing yield through such manipulations is met by Zhang who teaches the crossing of staygreen phenotypes results in increased yield [p.2272, ‘Summary’; p.2280, col.2, par.1].
Increased amount of harvested grain results from increased number of ears on plants (i.e. ‘increased flower number’), more grains per ear (i.e. ‘increased ear length’), and/or increased size of seeds produced by ears (i.e. ‘increased size of floral structures’).
As such, broadest reasonable interpretation of the claim language is that increased grain contributed by increased flower number and/or floral structure size encompasses ‘increased yield’ even if Applicant does not use the term verbatim in claim 16, or report phenotype as bushel per acre per se.
Although Zhang does not explicitly state the exact positional numberings of Applicant’s claims verbatim, when producing the same functional protein such specificity represents a mere design choice in routine replication of a known allele. One would be motivated to recreate the same mutant protein by altering sequence in slightly different locations within the reported NAC7 gene model GRMZM2G114850 and corresponding ‘nactf108’ sequence. They would want to do this to develop alternate alleles of the same functional phenotype already in the public domain, because such alleles are acknowledged as agronomically and economically valuable. At the time of filing, it was known in the art that truncating the NAC7 protein would be a way to do the same thing as already occurs in the germplasm reported by Zhang.
Conclusion
No claims are 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 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
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