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 .
Status of the Claims
Claims 2-9, 11-12, 19, 21-32, 34-54, 56-58, 60-61, 63, 65-69, 72-74, 76-87, 89-92, 94, and 96-110 are canceled.
Claims 1, 10, 13-18, 20, 33, 55, 59, 62, 64, 70 71, 75, 88, 93, and 95 are pending.
Claims 55, 59, 62, 64, 70 71, 75, 88, 93, and 95 are withdrawn from consideration.
Claims 1, 10, 13-18, 20, and 33 are elected and examined herein.
Claims 1, 10, 13-18, 20, and 33 are rejected.
Election/Restrictions
Applicant’s election without traverse of Group I, encompassing claims 1, 10, 13-18, 20, and 33 and Applicant’s election of SEQ ID NOs: 78, 108, 80, 124, and 125 in the reply filed on 01/19/2026 is acknowledged.
Priority
Application No. 18/442,164 filed on 02/15/2024 claims priority to provisional Application No. 63/485,263 filed on 02/16/2023.
Claim Objections
Claim 1 recites:
A corn plant or plant part thereof comprising at least one mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor:
(a) comprises a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs: 69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprises a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encodes a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71,74, 77, 80, or 83; and/or
(d) encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113 and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof.
As written, the limitation in part (d) that reads “and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof” appears to only be required if the endogenous gene encoding the PIF transcription factor encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113 (i.e. part (d)). However, it is reasonably interpreted that this limitation is meant to be applied if the endogenous PIF gene comprises any of (a) through (d).
To improve clarity, Applicant should amend the claim so that “and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof” is a wherein clause. With the suggested amendment, the claim would read:
A corn plant or plant part thereof comprising at least one mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor:
(a) comprises a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs: 69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprises a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encodes a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71,74, 77, 80, or 83; and/or
(d) encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113;
wherein the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof.
Claim 17 recites:
The corn plant or plant part of claim 1, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more plants, optionally exhibiting at least one of the following phenotypes of increased yield, decreased height, decreased shoot:root ratio, decreased leaf length; increased mechanical strength of stems; reduced lodging rate; delayed senescence; increased photosynthesis efficiency and grain filling; and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more plants as compared to a corn plant that does not comprise a reduced Shade Avoidance Response when planted in close proximity with one or more plants.
Claim 17 is objected to because of the inconsistency of punctuation that makes the claim difficult to read/ follow. The claim begins with using commas (,) but switches to semi-colons (;) in the middle of the claim. Applicant should amend the claim to address this deficiency.
Claim 33 recites:
A corn plant regenerated from the plant part of claim 1 and comprising the mutation in the endogenous gene encoding the PIF transcription factor, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more corn plants, optionally exhibiting at least one of the following phenotypes of increased yield, decreased height, decreased shoot:root ratio, decreased leaf length; increased mechanical strength of stems; reduced lodging rate; delayed senescence; increased photosynthesis efficiency and grain filling; and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more corn plants as compared to a corn plant that does not comprise a reduced Shade Avoidance Response that is when planted in close proximity with one or more corn plants, optionally wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis.
Claim 33 is objected to because of the inconsistency of punctuation that makes the claim difficult to read/ follow. The claim begins with using commas (,) but switches to semi-colons (;) in the middle of the claim. Applicant should amend the claim to address this deficiency.
Improper Markush Grouping
Claims 1 and 20 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of
SEQ ID NOs: 69, 70, 72, 73, 75, 76, 78, 79, 81, or 82 (claim 1)
SEQ ID NOs: 84-87, 88-91, 92-95, 96-108 or 109-112 (claim 1)
SEQ ID NOs: 71,74, 77, 80, or 83 (claim 1)
SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, or 135 encoding SEQ ID NOs:121, 123, 125, 127, or 131 (claim 20)
is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
Regarding group i), the sequences are either genomic DNA or cDNA of different corn PIF genes (spec, p. 106, lines 28-31) that do not share a single structural similarity. An ABSS sequence search of elected SEQ ID NO: 78 (see file wrapper 20260219_110106_us-18-442-164-78.align45.rnpbm) which corresponds to the corn PIF gene Zm00001d033267 returned results having as low as 5% sequence identity to SEQ ID NO: 78. From the instant application, only edited versions of the Zm00001d033267 appeared in the results and had high sequence identity to SEQ ID NO: 78. Additionally, SEQ ID NO: 79 appeared in the results and had only 6.2% sequence identity oy SEQ ID NO: 78. All other sequences did not appear in the results, meaning they had below 5% sequence identity to instant SEQ ID NO: 78. That is, none of the other sequences in group i) listed above are structurally similar to SEQ ID NO: 78. Hence, the included species of the claimed invention, i.e. the other PIF genes, do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group ii), the sequences are DNA regions specific to distinct PIF genes described above. An ABSS sequence search of elected SEQ ID NO: 108 (see file wrapper 20260210_142753_us-18-442-164-108.rnpbm) returned results having as low as 41% sequence identity to SEQ ID NO: 108. From the instant application, only SEQ ID NOs: 96-99 and 105-108 appeared in the results and had high sequence identity to SEQ ID NO: 108. All other sequences did not appear in the results or did not have high sequence identity, meaning none of the other sequences in group ii) listed above are structurally similar to SEQ ID NO: 108. Hence, the included species of the claimed invention, i.e. the other regions of PIF genes, do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group iii), the sequences are amino acid sequence encoded by different PIF genes described above. An ABSS sequence search of elected SEQ ID NO: 80 (see file wrapper 20260210_142721_us-18-442-164-80.rapbm) returned results having as low as 19% sequence identity to SEQ ID NO: 80. From grouping, only SEQ ID NOs: 77 and 83 appeared in the results and had low sequence identity of about 22% to SEQ ID NO: 80. All other sequences in group iii) did not appear in the results, thus has less than 19% sequence identity to SEQ ID NO: 80. That is, none of the other sequences in group iii) listed above are structurally similar to SEQ ID NO: 80. Hence, the included species of the claimed invention, i.e. the other PIF polypeptides, do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group iv) the sequences are mutated DNA and encoded amino acid sequences of the different PIF genes (see Table 1 on p. 107-108) (e.g. SEQ ID NOs: 124, 128-129, and 132-134 are mutated sequences of SEQ ID NO: 78). For the same reasons previously set forth regarding the different PIF genes, the sequences do not all share both a substantial structural feature and a common function that flows from the substantial structural feature.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Rejections - 35 USC § 112
Written Description
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.
Claims 1, 10, 13-18, 20, and 33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are broadly drawn to a corn plant or plant part thereof comprising at least one mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor: (a) comprises a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs: 69, 70, 72, 73, 75, 76, 78, 79, 81, or 82; (b) comprises a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112; (c) encodes a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71,74, 77, 80, or 83; and/or (d) encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113 and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof (claim 1). Additionally, claim 20 is broadly drawn to the corn plant or plant part thereof of claim 1, wherein the at least one mutation results in a mutated PIF gene comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, or 135 and/or which encodes a mutated PIF polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:121, 123, 125, 127, or 131.
Regarding elected SEQ ID NO: 78, 108, 80, 124, and 125, Applicant describes in working examples using CRISPR/Cas guide nucleic acids to target a region of a PIF gene that is 100% identical to SEQ ID NO: 108 in corn (spec., p. 106-107). The gene comprising this region is 100% identical to SEQ ID NO: 78. The guide nucleic acids produced mutations at the targeted sites, resulting in sequences 100% identical to SEQ ID NOs: 124 and 125.
Applicant does not teach any DNA or amino acid sequence that is as low as 80% sequence identity to SEQ ID NOs: 78, 108, or 80 that is still able to confer the function of a PIF gene/polypeptide, nor any sequence of a PIF gene/ protein having as low as 90% sequence identity to SEQ ID NOs: 124 and 125 that would be recognized as a PIF gene/ polypeptide sequence.
The prior art fails to remedy this deficiency. Regarding elected SEQ ID NO: 78, which is a PIF gene identified as Zm00001d033267 in the specification (p. 106), there appears to be a dearth of description of the nucleotide sequences that would be expected to have the function of a PIF gene at as low as 80% sequence identity. A review of sequences that share identity with elected SEQ ID NO: 78 reveals a large identity gap between two sequential search results of SEQ ID NO: 78 (see file wrapper 20260219_110106_us-18-442-164-78.align45.rnpbm). Both search results are from the instant application, the first having 99.9% sequence identity and the next most similar having 76.1% sequence identity:
Result Query Filing
No. Score Match Length ID Date Dups Description
-------------------------------------------------------------------------------------
3 16773 99.9 16786 US-18-442-164-129 2024-02-15 1 METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS (en)
4 12771 76.1 12785 US-18-442-164-128 2024-02-15 1 METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS (en)
SEQ ID NO: 108 is a region of SEQ ID NO: 78 and the prior art fails to remedy the deficiency for the same reason.
Regarding elected SEQ ID NO: 80, which is a PIF polypeptide sequence encoded by SEQ ID NO: 78 according to the spec (p. 8), there appears to be a dearth of description of the polypeptide sequences that would be expected to have the function of a PIF protein at as low as 80% sequence identity. A review of sequences that share identity with elected SEQ ID NO: 80 reveals a large identity gap between sequential search results of SEQ ID NO: 80 (see file wrapper 20260210_142721_us-18-442-164-80.rapbm), where the sequences also fail to describe the sequences as PIF polypeptides. Specifically, no sequences between result 1 and result 6 describe the polypeptide as being a PIF polypeptide. Additionally, a large identity gap exists between result 6 which has 91.4% sequence identity and result 7 which has 67% sequence identity to SEQ ID NO: 80.
Result Query Filing
No. Score Match Length ID Date Dups
1 2973 100.0 566 US-14-628-469-49413 2015-02-23 2 NOVEL TRANSCRIPTS AND USES THEREOF FOR IMPROVEMENT OF AGRONOMIC CHARACTERISTICS
2 2937 98.8 562 US-14-419-264A-727 2015-02-03 1 PHOTOSYNTHETIC RESOURCE USE EFFICIENCY IN PLANTS EXPRESSING REGULATORY PROTEINS
3 2855 96.0 543 US-15-047-804-162205 2016-02-19 0 NOVEL ALTERNATIVELY SPLICED TRANSCRIPTS AND USES THEREOF FOR IMPROVEMENT OF AGRO
4 2819 94.8 539 US-15-047-804-162206 2016-02-19 0 NOVEL ALTERNATIVELY SPLICED TRANSCRIPTS AND USES THEREOF FOR IMPROVEMENT OF AGRO
5 2814 94.7 539 US-11-241-607-60267 2005-09-30 3 SEQUENCE-DETERMINED DNA FRAGMENTS AND CORRESPONDING POLYPEPTIDES
6 2717 91.4 521 US-18-442-164-125 2024-02-15 1 METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS (en)
7 1991.5 67.0 532 US-14-419-264A-733 2015-02-03 0 PHOTOSYNTHETIC RESOURCE USE EFFICIENCY IN PLANTS EXPRESSING REGULATORY PROTEINS
Regarding elected SEQ ID NO: 124, which is a mutated PIF nucleotide sequence where 3 basepairs has been deleted from SEQ ID NO: 78 according the specification (p. 106), there appears to be a dearth of description of the nucleotide sequences that would be expected to have the function of a PIF gene at as low as 90% sequence identity with or without the 3 bp mutation, or be recognized as a PIF nucleotide sequence. A review of sequences that share identity with elected SEQ ID NO: 124 reveals a large identity gap between two sequential search results (see file wrapper 20260220_090848_us-18-442-164-124.align45.rnpbm). Both search results are from the instant application, the first having 99.9% sequence identity and the next most similar having 76.1% sequence identity:
Result Query Filing
No. Score Match Length ID Date Dups Description
------------------------------------------------------------------------------
3 16773 99.9 16789 US-18-442-164-78 2024-02-15 1 METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS (en)
4 12774 76.1 12785 US-18-442-164-133 2024-02-15 1 METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS (en)
Regarding elected SEQ ID NO: 125, which is a polypeptide encoded by a mutated PIF nucleotide sequence where 3 basepairs has been deleted from SEQ ID NO: 78 according the specification (p. 106), there appears to be a dearth of description of the polypeptide sequences that would be expected to have the function of a PIF polypeptide at as low as 90% sequence identity with or without the removal of a the splice site that results from the 3 bp deletion from SEQ ID NO: 78, or be recognized as a PIF polypeptide sequence. A review of sequences that share identity with elected SEQ ID NO: 125 reveals a large identity gap between two sequential search results (see file wrapper 20260210_142831_us-18-442-164-125.rapbm), the first having 97.7% sequence identity and the next most similar having 67.1% sequence identity:
Result Query Filing
No. Score Match Length ID Date Dups
------------------------------------------------------------------------------------
6 2676 97.7 539 US-11-241-607-60267 2005-09-30 3 SEQUENCE-DETERMINED DNA FRAGMENTS AND CORRESPONDING POLYPEPTIDES
7 1837.5 67.1 532 US-14-419-264A-733 2015-02-03 0 PHOTOSYNTHETIC RESOURCE USE EFFICIENCY IN PLANTS EXPRESSING REGULATORY PROTEINS
The instant specification does not provide enough sequences to describe the
genus of regulatory sequences at as low as 80% or 90% sequence identity by
virtue of example. There also is a dearth of description in the prior art of the elected sequences that would be expected to have the required function of a PIF gene or polypeptide. As such, the structural features that distinguish nucleotides or polypeptides with as low as 80% or 90% identity to SEQ ID NOs: 78, 108, 80, 124, and 125 that are PIF sequences from other nucleotides or polypeptides with 80% or 90% identity to SEQ ID NOs: 78, 108, 80, 124, and 125 are not described in the specification nor the prior art. The specification fails to provide an adequate written description to support the sequences recited in claims 1 and 20 with 80% or 90% identity that are able to effectively confer the functions of a PIF gene or protein. The limited examples of 100% identity to the recited sequences do not describe the claimed genus by virtue of example. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 10, 13-18, and 33 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.) and as evidenced by maizeGDB GRMZM2G165042 (maizeGDB, GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43), B73 RefGen_v3, published online and last update7 07/23/2017).
Claim 1 is drawn to a corn plant or plant part thereof comprising at least one mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor:
(a) comprises a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprises a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encodes a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71,74, 77, 80, or 83; and/or (d) encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113 and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof.
Claim 10 is drawn to the corn plant or plant part thereof of claim 1, wherein the at least one mutation is a base substitution, a base deletion and/or a base insertion.
Claim 13 is drawn to the corn plant or plant part thereof of claim 1, wherein the at least one mutation is a base deletion.
Claim 14 is drawn to the corn plant or plant part thereof of claim 13, wherein the deletion is an in-frame or an out-of-frame deletion.
Claim 15 is drawn to the corn plant or plant part thereof of claim 13, wherein the deletion is deletion of 1 to 10 nucleotides.
Claim 16 is drawn to the corn plant or plant part thereof of claim 13, wherein the deletion generates an early stop codon.
Claim 17 is drawn to the corn plant or plant part of claim 1, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more plants, optionally exhibiting at least one of the following phenotypes of increased yield, decreased height, decreased shoot:root ratio, decreased leaf length; increased mechanical strength of stems; reduced lodging rate; delayed senescence; increased photosynthesis efficiency and grain filling; and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more plants as compared to a corn plant that does not comprise a reduced Shade Avoidance Response when planted in close proximity with one or more plants.
Claim 18 is drawn to the corn plant or plant part thereof of claim 1, wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis, optionally wherein the planting density is increased by about 5% to about 75% without a decrease in plant yield on a per plant basis.
Claim 33 is drawn to the corn plant regenerated from the plant part of claim 1 and comprising the mutation in the endogenous gene encoding the PIF transcription factor, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more corn plants, optionally exhibiting at least one of the following phenotypes of increased yield, decreased height, decreased shoot:root ratio, decreased leaf length; increased mechanical strength of stems; reduced lodging rate; delayed senescence; increased photosynthesis efficiency and grain filling; and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more corn plants as compared to a corn plant that does not comprise a reduced Shade Avoidance Response when planted in close proximity with one or more corn plants, optionally wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis.
Regarding claim 1, Wu discloses knocking out PIF3, PIF4, and PIF5 genes in maize plants via CRISPR/Cas9-mediated editing to induce mutations (abstract, p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize). Because the genes are knocked out, the mutations are reasonably interpreted to disrupt the binding of the PIF transcription factors to DNA in the corn plant. Wu also discloses the Zmpif4.1 and Zmpif4.2 double knockout mutants (p. 796, section titled Knockout of ZmPIFs by CRISPR/Cas9 Causes Short Mesocotyls in Maize under Darkness) comprised mutations to sequences of Zmpif4.1 (GRMZM5G86596) and Zmpif4.2 (GRMZM2G165042). GRMZM2G165042 has an amino acid sequence that is 99% identical to instant SEQ ID NO: 80 as evidenced by maizeGDB (see attached reference and alignment below). Therefore, Wu discloses the instantly claimed invention of a corn plant comprising at least one mutation to an endogenous PIF transcription factor comprising a sequence at least 80% identical to elected SEQ ID NO: 80, wherein the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant.
PNG
media_image1.png
703
806
media_image1.png
Greyscale
Regarding claims 10 and 13, Wu discloses generating ZmPIF knockout lines via Cas9-mediated targeted deletion (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize) to delete nucleotides from the endogenous genes (Supplementary Fig. 12).
Regarding claim 14, Wu discloses a 322 bp deletion and a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash). The 322 bp deletion would result in an out of frame mutation (322/3=107.33). A single basepair deletion results in an out of frame mutation. Therefore, in either case, the deletions in ZmPIF4.2 disclosed by Wu produce out of frame mutations.
Regarding claim 15, as stated above, Wu discloses a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash).
Regarding claim 16, Wu discloses a 322 bp deletion and a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash). Using the cDNA sequence of GRMZM2G165042 from maize GDB (beginning at the start codon) which is the sequence in the maize knockout line of Zmpif4s#65 (ZmPIF4.2-KO, MT in Supplementary Fig. 12), and deleting the exact 322 basepairs and the 1 nucleotide as disclosed by Wu in the Supplementary Figure, the resulting nucleotide sequence translates to a polypeptide sequence with multiple early stop codons as shown directly below. Asterisks represent stop codons.
MNQFVPDWSNTSRAAGTSQSQQRTTGAAAAGRARCRRGTRAT*CRLPSRRPRPAPGSRRR
*AWPTAATMPEGTCRASSVRGRRPARRRC*ARSGPASAGATRSWCSARRARRGARPRPAP
EPPAATGPGPPRCRRRWAARTRTPWAAAGATRRPRRGGPTTAASAPPPPQPQPPPRSPRA
PATGAASASGSTPRTRRVPARTRSRGPPRCWRASRRRR*RRRGGAAPPKCTTCRSGGDET
G*TRR*EPCVALSTSLSLSSQHSSSSRL*RVEEARSSHRGLQQPSALSIEAALCSLLSAL
PR*AGFQASSAECEL*LNTK*LAASHRSMVVLCWPSER*TSSSLIGATWETPPGRSAKKT
TSSSCYGATAMSSCRARATGRCRRGRRRRRQWRLHQPPRPCRRKTRAACGSPSRWPTRWT
RTSSRSSSARHRRRHRRRRMRRRRPLVVEPAPKPAASRAAGTSQSQQRTTGAAAAGRARC
RRGTRAT*CRLPSRRPRPAPGSRRR*AWPTAATMPEGTCRASSVRGRRPARRRC*ARSGP
ASAGATRSWCSARRARRGARPRPAPEPPAATGPGPPRCRRRWAARTRTPWAAAGATRRPR
RGGPTTAASAPPPPQPQPPPRSPRAPATGAASASGSTPRTRRVPARTRSRGPPRCWRASR
RRR*RRRGGAAPPKCTTCRSGGDETG*TRR*EPCKSSYLTATRRTRRQCLTRRSSTSSRC
SCKCR*CGWAAPASRRRRR*CSPAYTSTCLGWASGWARQRRRRCRPCRGCRSWPRNRWCP
ARR*AWARCRPTGATCPRWASRSRTGTTSASTTCSRRRRHRRSRA*ATTRRRWGRRRRPC
SRLQSFTTCRGPAAASCPPAPHPECCSRRARKAEGQVRCHALRPSHPPLQFLGYKWEHYD
Regarding claim 33, Wu discloses regenerating the transgenic lines with mutated PIF genes from transformed immature embryos (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize).
Claims 17-18 and the remaining limitation of claim 33 are also anticipated as a function of inherency. Wu discloses claim 1, requiring a mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor comprises a sequence with at least 80% sequence identity to SEQ ID NO: 80 (elected), and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof. Wu also discloses the wild-type maize seedlings exposed to simulated shade conditions displayed phenotypes characteristic of the shade avoidance response, but this response was attenuated in the Zmpifs mutants (i.e. reduce shade avoidance response) (abstract, p. 797 ¶2, Fig. 8, C and D). Claims 17, 18, and the remaining limitation of claim 33 require the corn plant or plant part of claim 1, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more plants (claim 17); the corn plant or plant part thereof of claim 1, wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis (claim 18); and wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more corn plants (remaining limitation of claim 33). Because Wu discloses knocking out a PIF4 gene encoding a PIF4 polypeptide (which is what SEQ ID NO: 80 is according to the spec., p. 8) that has over 99% sequence identity to instant SEQ ID NO: 80, and also discloses these plants had reduced shade avoidance response, the corn plant with the PIF4 knockout disclosed by Wu would be reasonably interpreted to be capable of the same recited function that is i. reduced Shade Avoidance Response when planted in close proximity with one or more plants and ii. capable of being planted at an increased density without a decrease in plant yield on a per plant basis as required by claims 17 and 18.
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 20 is rejected under 35 U.S.C. 103 as being unpatentable over Wu and maizeGDB GRMZM2G165042 as applied to claim 1, and further in view of Li (Li, J., Li, Y., & Ma, L. (2019). CRISPR/Cas9‐based genome editing and its applications for functional genomic analyses in plants. Small Methods, 3(3), 1800473.) and GenBank accession No. DAA50359 (GenBank accession No. DAA50359, putative HLH DNA-binding domain superfamily protein, published online 10/24/2013).
Claim 20 is drawn to 20 the corn plant or plant part thereof of claim 1, wherein the at least one mutation results in a mutated PIF gene comprising a nucleotide sequence having at least 90% sequence identity to any one of SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, or 135 and/or which encodes a mutated PIF polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:121, 123, 125, 127, or 131.
Regarding claim 20, Wu teaches the limitations of claim 1 as set forth in the previous anticipation rejection. The teachings of Wu as they are applied to claim 1 are set forth previously herein and are incorporated by reference. Specifically, Wu teaches generating PIF4 double knockout in maize plants (p. 796). One of the PIF4 sequences, GRMZM2G165042 which encodes a polypeptide sequence that is over 99% identical to instant SEQ ID NO: 80, is knocked out by inducing two mutations: one being a 322 bp deletion and the other a single nucleotide deletion (Supplementary Fig. 12, Zmpif4s#65, ZmPIF4.2-KO, MT sequence) in the sequence of GRMZM2G165042 in maize plants (p. 796 and 801). Wu teaches the knockout lines display reduced shade avoidance response as compared to WT control plants (abstract, p. 797 ¶2, Fig. 8, C and D).
However, Wu does not appear to explicitly teach wherein the at least one mutation results in a mutated PIF gene comprising a nucleotide sequence which encodes a mutated PIF polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:121, 123, 125, 127, or 131.
It is noted that SEQ ID NO: 125 is derived from SEQ ID NO: 80, having 22 amino acid residues removed at positions 344-365 of SEQ ID NO: 80.
In analogous art, Li teaches CRISPR/Cas9 has been widely used to create various mutants and become a routine tool in plant laboratories around the world (p. 8) including knockouts and fragment deletions (Fig. 7). Furthermore, the polypeptide sequence of GRMZM2G165042 is linked in the maizeGDB database as GenBank accession No. DAA50359 which identifies amino acid residues 333 to 394 as the bHLH domain.
Because Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduce shade avoidance response, and methods of knocking out and deleting fragments from genes/ proteins are routine and known in the art, it would be prima facie obvious to target and remove any sequence of the known gene/protein to knockout the gene for the purpose of reducing shade avoidance response and in turn increasing yield as taught by Wu (abstract). This is especially true for the known amino acid residues that make up the bHLH domain as identified by GenBank Accession No. DAA50359. Therefore, it would be prima facie obvious to delete the 22 amino acid residues from the polypeptide sequence of SEQ ID NO: 80 which are within the bHLH domain according to GenBank Accession No. DAA50359 to arrive at SEQ ID NO: 125 for the purpose of knocking out the function of the polypeptides. One of ordinary skill in the art would have a reasonable expectation of success because generating knockouts via various methods is well understood and routine in the art, and one of ordinary skill in the art would expect that deletion of a segment as large as 22 amino acids from the identified bHLH domain that is approximately 66 residues long (i.e. removing a third of the bHLH domain) could reasonably be expected to knockout the gene and encoded protein.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 54, 55, and 64 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7, 9, 12, 13, and 14 of copending Application No. 18664349 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 10, 13-18, and 33 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7, 10, and 11 of copending Application No. 18664349 in view of Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.) and as evidenced by maizeGDB GRMZM2G165042 (maizeGDB, GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43).
Regarding claim 1, 18664349 teaches a method for editing a specific site in the genome of a plant cell, the method comprising introducing a gene editing system into the plant cell, the gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to a Phytochrome Interacting Factor (PIF) gene and the CRISPR-Cas effector protein cleaving, in a site-specific manner, a target site within an endogenous Phytochrome Interacting Factor (PIF) gene in the plant cell, the endogenous PIF gene: (a) comprising a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82; (b) comprising a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112; (c) encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71, 74, 77, 80, or 83; and/or (d) encoding a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113, thereby generating an edit in the endogenous PIF gene of the plant cell (claim 1 of 18664349). 18664349 further teaches regenerating a plant from the plant cell comprising the edit in the endogenous PIF gene to produce a plant comprising the edit in its endogenous PIF gene (claim 10 of 18664349).
Regarding claim 17, 18664349 teaches wherein the plant comprising the edit in its endogenous PIF transcription factor gene has an attenuated Shade Avoidance Response compared to a control plant that is devoid of the edit (claim 11 of 18664349).
Regarding claim 33, 18664349 teaches regenerating a plant from the plant cell comprising the edit in the endogenous PIF gene to produce a plant comprising the edit in its endogenous PIF gene (claim 10 of 18664349); and teaches wherein the plant comprising the edit in its endogenous PIF transcription factor gene has an attenuated Shade Avoidance Response compared to a control plant that is devoid of the edit (claim 11 of 18664349).
However, 18664349 does not explicitly teach:
the plant is a corn plant, and the mutation disrupts the binding of the PIF transcription factor to DNA in the corn plant (remaining limitation of claim 1)
The corn plant or plant part thereof of claim 1, wherein the at least one mutation is a base substitution, a base deletion and/or a base insertion (claim 10)
The corn plant or plant part thereof of claim 1, wherein the at least one mutation is a base deletion (claim 13)
The corn plant or plant part thereof of claim 13, wherein the deletion is an in-frame or an out-of-frame deletion (claim 14)
The corn plant or plant part thereof of claim 13, wherein the deletion is deletion of 1 to 10 nucleotides (claim 15)
The corn plant or plant part thereof of claim 13, wherein the deletion generates an early stop codon (claim 16)
wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more plants (remaining limitation of claim 17)
wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis, optionally wherein the planting density is increased by about 5% to about 75% without a decrease in plant yield on a per plant basis (claim 18)
the corn plant regenerated from the plant part of claim 1 and comprising the mutation in the endogenous gene encoding the PIF transcription factor, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more corn plants, optionally exhibiting at least one of the following phenotypes of increased yield, decreased height, decreased shoot:root ratio, decreased leaf length; increased mechanical strength of stems; reduced lodging rate; delayed senescence; increased photosynthesis efficiency and grain filling; and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more corn plants as compared to a corn plant that does not comprise a reduced Shade Avoidance Response when planted in close proximity with one or more corn plants (remaining limitation of claim 33)
Regarding claim 1, In analogous art, Wu teaches knocking out PIF3, PIF4, and PIF5 genes in maize plants via CRISPR/Cas9-mediated editing to induce mutations (abstract, p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize). Because the genes are knocked out, the mutations are reasonably interpreted to disrupt the binding of the PIF transcription factors to DNA in the corn plant. Wu also teaches the Zmpif4.1 and Zmpif4.2 double knockout mutants (p. 796, section titled Knockout of ZmPIFs by CRISPR/Cas9 Causes Short Mesocotyls in Maize under Darkness) comprised mutations to sequences of Zmpif4.1 (GRMZM5G86596) and Zmpif4.2 (GRMZM2G165042). GRMZM2G165042 has an amino acid sequence that is 99% identical to instant SEQ ID NO: 80 as evidenced by maizeGDB. Therefore, Wu teaches the instantly claimed invention of a corn plant comprising at least one mutation to an endogenous PIF transcription factor comprising a sequence at least 80% identical to elected SEQ ID NO: 80, wherein the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant.
Regarding claims 10 and 13, Wu teaches generating ZmPIF knockout lines via Cas9-mediated targeted deletion (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize) to delete nucleotides from the endogenous genes (Supplementary Fig. 12).
Regarding claim 14, Wu teaches a 322 bp deletion and a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash). The 322 bp deletion would result in an out of frame mutation (322/3=107.33). A single basepair deletion results in an out of frame mutation. Therefore, in either case, the deletions in ZmPIF4.2 taught by Wu produce out of frame mutations.
Regarding claim 15, as stated above, Wu teaches a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash).
Regarding claim 16, Wu teaches a 322 bp deletion and a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash). Using the cDNA sequence of GRMZM2G165042 from maize GDB (beginning at the start codon) which is the sequence in the maize knockout line of Zmpif4s#65 (ZmPIF4.2-KO, MT in Supplementary Fig. 12), and deleting the exact 322 basepairs and the 1 nucleotide as disclosed by Wu in the Supplementary Figure, the resulting nucleotide sequence translates to a polypeptide sequence with multiple early stop codons.
Regarding claim 33, Wu teaches regenerating the transgenic lines with mutated PIF genes from transformed immature embryos (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize).
Claims 17-18 and the remaining limitation of claim 33 are also obvious as a function of inherency. Wu teaches claim 1, requiring a mutation in an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encoding the PIF transcription factor comprises a sequence with at least 80% sequence identity to SEQ ID NO: 80 (elected), and the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof. Wu also teaches the wild-type maize seedlings exposed to simulated shade conditions displayed phenotypes characteristic of the shade avoidance response, but this response was attenuated in the Zmpifs mutants (i.e. reduce shade avoidance response) (abstract, p. 797 ¶2, Fig. 8, C and D). Claims 17, 18, and the remaining limitation of claim 33 require the corn plant or plant part of claim 1, wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more plants (claim 17); the corn plant or plant part thereof of claim 1, wherein the corn plant is capable of being planted at an increased density without a decrease in plant yield on a per plant basis (claim 18); and wherein the corn plant exhibits reduced Shade Avoidance Response when planted in close proximity with one or more corn plants (remaining limitation of claim 33). Because Wu teaches knocking out a PIF4 gene encoding a PIF4 polypeptide (which is what SEQ ID NO: 80 is according to the spec., p. 8) that has over 99% sequence identity to instant SEQ ID NO: 80, and also teaches these plants had reduced shade avoidance response, the corn plant with the PIF4 knockout taught by Wu would be reasonably interpreted to be capable of the same recited function that is i. reduced Shade Avoidance Response when planted in close proximity with one or more plants and ii. capable of being planted at an increased density without a decrease in plant yield on a per plant basis as required by claims 17 and 18.
It would be obvious to combine the teachings of 18664349 with Wu because both are directed to mutating the same endogenous sequence to attenuate shade avoidance response, and Wu applies the method to corn plants. One of ordinary skill in the art would have a reasonable expectation of success because Wu teaches the claimed method of 18664349 applied to corn plants effectively confers the trait of attenuated shade avoidance response.
This is a provisional nonstatutory double patenting rejection.
Claim 20 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7, 9, 10, and 11 of copending Application No. 18664349 in view of Wu and maizeGDB GRMZM2G165042 as applied previously herein, and further in view of Li (Li, J., Li, Y., & Ma, L. (2019). CRISPR/Cas9‐based genome editing and its applications for functional genomic analyses in plants. Small Methods, 3(3), 1800473.) GenBank accession No. DAA50359 (GenBank accession No. DAA50359, putative HLH DNA-binding domain superfamily protein, published online 10/24/2013).
Regarding claim 20, 18664349, Wu, and maizeGDB GRMZM2G165042 teach the limitations of claim 1 as set forth in the previous NSDP rejection. The teachings of 18664349, Wu, and maizeGDB GRMZM2G165042as they are applied to claim 1 are set forth previously herein and are incorporated by reference. Furthermore 18664349 also teaches wherein the edit results in a mutation in the basic Helix Loop Helix (bHLH) domain of the PIF polypeptide encoded by the endogenous PIF gene (claim 9 of 18664349).
However, Wu does not appear to explicitly teach wherein the at least one mutation results in a mutated PIF gene comprising a nucleotide sequence which encodes a mutated PIF polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:121, 123, 125, 127, or 131.
It is noted that SEQ ID NO: 125 is derived from SEQ ID NO: 80, having 22 amino acid residues removed at positions 344-365 of SEQ ID NO: 80.
In analogous art, Li teaches CRISPR/Cas9 has been widely used to create various mutants and become a routine tool in plant laboratories around the world (p. 8) including knockouts and fragment deletions (Fig. 7). Furthermore, the polypeptide sequence of GRMZM2G165042 is linked in the maizeGDB database as GenBank accession No. DAA50359 which identifies amino acid residues 333 to 394 as the bHLH domain.
Because 18664349 teaches an identical method (although not in corn plants), and Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduce shade avoidance response in corn, and methods of knocking out and deleting fragments from genes/ proteins are routine and known in the art, it would be prima facie obvious to target and remove any sequence of the known gene/protein to knockout the gene for the purpose of reducing shade avoidance response and in turn increasing yield as taught by Wu (abstract). This is especially true for the known amino acid residues that make up the bHLH domain as identified by GenBank Accession No. DAA50359. Therefore, it would be prima facie obvious to delete the 22 amino acid residues from the polypeptide sequence of SEQ ID NO: 80 which are within the bHLH domain according to GenBank Accession No. DAA50359 to arrive at SEQ ID NO: 125 for the purpose of knocking out the function of the polypeptides. One of ordinary skill in the art would have a reasonable expectation of success because generating knockouts via various methods is well understood and routine in the art, and one of ordinary skill in the art would expect that deletion of a segment as large as 22 amino acids from the identified bHLH domain that is approximately 66 residues long (i.e. removing a third of the bHLH domain) could reasonably be expected to knockout the gene and encoded protein.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA N STOCKDALE whose telephone number is (703)756-5395. The examiner can normally be reached M-F 8:30-5:00 CT.
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 Abraham can be reached at (571) 270-7058. 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.
JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
Prosecution Insights