METHODS AND COMPOSITIONS FOR MODIFYING SHADE AVOIDANCE IN PLANTS

§102 §103 §112 §DOUBLEPATENT

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 Claims 55, 59, 62, 64, 70 71, 75, 88, 93, and 95 are withdrawn from consideration.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 examined herein. Claims 1, 10, 13-18, 20, and 33 are rejected. 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. This is a modified rejection from the rejection set forth in the previous Office Action dated 04/22/2026, necessitated by Applicant’s amendments. 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; wherein the PIF transcription factor comprises a basic Helix Loop Helix (bHLH) domain comprising the amino acid sequence of SEQ ID NO:113 and the at least one mutation is: (1) an in-frame deletion, and/or (2) a mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor, and wherein the at least one 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 endogenous corn PIF sequences at as low as 80% sequence identity or mutated PIF genes with as 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 § 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, 10, 13, 15-18, 20, and 33 are rejected under 35 U.S.C. 103 as being unpatentable over 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.), 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 bHLH DNA-binding domain superfamily protein, published online 10/24/2013), and as evidenced by maizeGDB GRMZM2G165042 (maizeGDB, GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43), B73 RefGen_v3, published online and last update7 07/23/2017). This is a modified rejection from the rejection set forth in the Office Action dated 04/22/2026, necessitated by Applicant’s amendments. Regarding claim 1, Wu teaches knocking out PIF3, PIF4, and PIF5 genes in maize plants via CRISPR/Cas9-mediated editing to induce deletion mutations in the target gene (abstract, p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, supplementary Fig. 12). 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 (see attached reference and alignment below). 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. Furthermore, GRMZM2G165042 also comprises a bHLH domain comprising SEQ ID NO: 113 (VHNLSERRRRD) as evidenced in the sequence alignment below. PNG media_image1.png 703 806 media_image1.png Greyscale 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) that produce out of frame mutations. 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 (i.e. wherein the base deletion generates an early stop codon). 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). However, Wu does not explicitly teach: the at least one mutation is: (1) an in-frame deletion, and/or (2) a mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor (remaining limitation of claim 1) wherein the mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor comprises a base substitution, a base deletion, or a base insertion (claim 10) wherein the mutation that removes part, but not all of, the amino acids of SEO ID NO:113 from the PIF transcription factor is a base deletion (claim 13) wherein the in frame deletion is deletion of 3, 6, or 9 (claim 15) 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 (claim 20) 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 annotates amino acid residues 333 to 394 as the bHLH domain. The sequence of instant SEQ ID NO: 113 is comprised within this annotated bHLH domain (positions 337 to 348). Because Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduced shade avoidance response, and because 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 annotated by GenBank Accession No. DAA50359 (which maizeGDB GRMZM2G165042 is linked to in the maizeGDB website), because DAA50359 is defined as a bHLH protein and the bHLH domain would have been understood by the ordinary artisan to be essential to the function of the polypeptide.. Therefore, it would be prima facie obvious to delete fragments of the bHLH domain (either in or out of frame) including 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. It is noted the mutation required to arrive at instant SEQ ID NO: 125 comprises removing part of SEQ ID NO: 113 via deletion mutation (satisfying claims 1, 10, 13 and 20). A 9 bp deletion of the known and conserved bHLH domain would also be obvious and expected by the ordinary artisan to disrupt polypeptide PIF function (as required in claim 15). 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 9 or 22 amino acids from the identified bHLH domain that is approximately 66 residues long (i.e. removing approximately 14-33% of the conserved bHLH domain) could reasonably be expected to knockout the gene and encoded protein. Claims 17-18 and the remaining limitation of claim 33 are also obvious as a function of inherency. Wu, Li, and GenBank accession No. DAA50359 teach 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 comprises SEQ ID NO: 113, and part of SEQ ID NO: 113 is removed as a result of mutation (see 103 above), 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, Li, and GenBank accession No. DAA50359 teach the obvious plant and method of 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 taught by Wu, Li, and GenBank accession No. DAA50359 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. 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 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). This is a maintained rejection. 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, 20, and 33 are 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 (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.), 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 bHLH DNA-binding domain superfamily protein, published online 10/24/2013), and as evidenced by maizeGDB GRMZM2G165042 (maizeGDB, GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43), B73 RefGen_v3, published online and last update7 07/23/2017). This is a modified rejection, necessitated by Applicant’s amendments. 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 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). 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 at least some limitations in claims 1, 10, 13-18, 20, and 33. In analogous art, Wu teaches knocking out PIF3, PIF4, and PIF5 genes in maize plants via CRISPR/Cas9-mediated editing to induce deletion mutations in the target gene (abstract, p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, supplementary Fig. 12). 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 (see attached reference and alignment below). 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. Furthermore, GRMZM2G165042 also comprises a bHLH domain comprising SEQ ID NO: 113 (VHNLSERRRRD) as evidenced in the sequence alignment below. PNG media_image1.png 703 806 media_image1.png Greyscale 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) that produce out of frame mutations. 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 as shown directly below (i.e. wherein the base deletion generates an early stop codon). 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 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). In other 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 annotates amino acid residues 333 to 394 as the bHLH domain. The sequence of instant SEQ ID NO: 113 is comprised within this annotated bHLH domain (positions 337 to 348). 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. 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 reduced shade avoidance response, and because 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 annotated by GenBank Accession No. DAA50359 (which maizeGDB GRMZM2G165042 is linked to in the maizeGDB website), because DAA50359 is defined as a bHLH protein and the bHLH domain would have been understood by the ordinary artisan to be essential to the function of the polypeptide.. Therefore, it would be prima facie obvious to delete fragments of the bHLH domain (either in or out of frame) including 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. It is noted the mutation required to arrive at instant SEQ ID NO: 125 comprises removing part of SEQ ID NO: 113 via deletion mutation (satisfying claims 1, 10, 13 and 20). A 9 bp deletion of the known and conserved bHLH domain would also be obvious and expected by the ordinary artisan to disrupt polypeptide PIF function (as required in claim 15). 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 9 or 22 amino acids from the identified bHLH domain that is approximately 66 residues long (i.e. removing approximately 14-33% of the conserved bHLH domain) could reasonably be expected to knockout the gene and encoded protein. Response to Arguments Applicant argues beginning on p. 8 of remarks dated 07/22/2026 the following arguments: I. Claim Objections A. Claim 1 is objected to for lacking clarity with regard to reciting in part (d) that the mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof. See Office Action, page 3. Claim 1 is amended herein to recite that the at least one mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof in a wherein clause, as suggested at page 4 of the Office Action. Withdrawal of the objection to claim 1 is therefore respectfully requested. B. Claims 17 and 33 are objected to because of an inconsistency of punctuation. See Office Action, page 4. Claims 17 and 33 are amended herein to consistently use commas between the phenotypes listed in these claims. Withdrawn claim 71 is amended in a similar manner. Withdrawal of the objection to claims 17 and 33 is therefore respectfully requested. Examiner’s Response: The objections have been withdrawn in view of Applicant’s amendments. Applicant argues beginning on p. 8 of remarks dated 07/22/2026 the following arguments: II. Improper Markush Grouping Rejection Claims 1 and 20 are rejected on the basis that they contain an improper Markush grouping of alternatives. See Office Action, page 5. Reconsideration is respectfully requested. Applicant respectfully disagrees with this rejection and submits that the Manual of Patent Examining Procedure (MPEP) states: A Markush claim may be rejected under judicially approved "improper Markush grouping" principles when the claim contains an improper grouping of alternatively useable members. A Markush claim contains an "improper Markush grouping" if either: (1) the members of the Markush group do not share a "single structural similarity" or (2) the members do not share a common use. Supplementary Guidelines at 7166 (citing In re Harnisch, 631 F.2d 716, 721-22, 206 USPQ 300, 305 (CCPA 1980)). MPEP § 2117(II) (emphasis added). A Markush grouping is ordinarily proper if all the members of the group belong to a recognized class (whether physical, chemical, or art recognized) and are disclosed in the specification to possess at least one property in common which is mainly responsible for their function in the claimed invention, and it is clear from their very nature or from the prior art that all members possess this property. MPEP § 2117(II)(A) (emphasis added). 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 explained in subsection II.A, above, the members of the Markush grouping may still be considered to be proper where the alternatives share a substantial structural feature that is essential to a common use. MPEP § 2117(II)(B) (emphasis added). Applicant respectfully submits that the group of sequences as recited in claim 1 is proper because the polynucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, 82, 84- 87, 88-91, 92-95, 96-108 and 109-112 all belong to a single art-recognized class of polynucleotides encoding a Phytochrome Interacting Factor (PIF) transcription factor and SEQ ID NOs:71, 74, 77, 80, and 83 all belong to a single art-recognized class of a PIF transcription factor polypeptide that regulates responses to illumination in plants (e.g., shade avoidance response (SAR)). See Specification, page 47, line 21. Similarly, the group of sequences as recited in claim 20 is proper because the polynucleotide sequences of SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, and 135 all belong to a single art-recognized class of polynucleotides encoding a mutant PIF transcription factor polypeptide and SEQ ID NOs:121, 123, 125, 127, and 131 all belong to a single art-recognized class of a mutant PIF transcription factor polypeptide. Further, each of the PIF transcription factor polypeptides possesses the common property of having a basic Helix Loop Helix (bHLH) domain and a conserved VHNLSERRRRD (SEQ ID NO:113) sequence motif, which is responsible for the common property of DNA binding and dimer formation. See Specification, page 47, lines 28-30. In addition, corn PIF transcription factor polypeptides are shown to have a phyB-binding domain, localize in the nucleus, interact with ZmphyB 1 and ZmphyB2, and form a transcription factor complex to promote cell elongation. See Specification, page 47, lines 23-27 and Wu et al. (2019), Figures 1, 2, and 4 (cited in the rejection under 35 U.S.C. § 102). Therefore, the disclosed PIF transcription factor polypeptides (1) have at least one property that the claimed sequences have in common, and (2) share at least one common structural feature and have a common use. The Patent Trial and Appeal Board (PTAB) agrees with Applicant's understanding of "a single structural similarity" and has on multiple occasions revisited the issue of an allegedly improper Markush group. See, e.g., Ex parte Narva, Appeal No. 2018-006168 (P.T.A.B. 2019) and Ex parte Ren, Appeal No. 2015-004371 (P.T.A.B. 2016). For example, in Ren, the Board reversed an improper Markush group rejection. Ren, Appeal No. 2015-004371, page 5. The Board in Ren held that a subgenus of trans-acting siRNAs with totally different nucleotide sequences, but with a shared nucleic acid backbone, were not improperly grouped, because they shared a "single structural similarity," and a common use. Ren, Appeal No. 2015-004371, page 4. More particularly, the Board in Ren held that "[m]embers of a Markush group share a 'single structural similarity' when they belong to the same recognized class," and that "[m]embers of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent." Ren, Appeal No. 2015-004371, page 4. Similar to Ren, the members of the claimed group of sequences each belong to the same art recognized class of being polynucleotides encoding PIF transcription factor polypeptides or being PIF transcription factor polypeptides that each include a bHLH domain characterized by the presence of a conserved VHNLSERRRRD (SEQ ID NO:113) sequence motif and aphyB-binding domain. In addition, each of the members of the claimed group of sequences is functionally equivalent as the polynucleotides each encode a PIF transcription factor polypeptide and the PIF transcription factor polypeptides each exhibit DNA binding, dimer formation, and transcription factor activity, and members of each group of sequences as claimed share the common use of promoting cell elongation. Further, in Narva, the PTAB reversed an improper Markush group rejection as the claimed species shared a single structural similarity and a common use. Narva, Appeal No. 2018-006168, page 4. In particular, the Board concluded that "the nucleic acid sequences recited in the rejected claims belong to the same recognized chemical class of polyribonucleotides that are hybridized in dsRNA molecules and encode ROP proteins. While the individual sequences differ because they are drawn to ROP sequences of different insects (e.g., SEQ ID NO:1 and 115) or different portions of the ROP sequence (e.g., SEQ ID NO:120, 131, and 133), all the sequences share the common use of silencing ROP proteins." Narva, Appeal No. 2018-006168, page 4 (emphasis added). Like Narva, the claimed polynucleotide and protein sequences may differ; however, all the sequences share the common use of, e.g, promoting cell elongation. The Federal Circuit has held that claims containing a Markush group should not be rejected as containing an improper grouping of alternative species if the species belong to a structural subgenus that Applicant describes as functionally equivalent, and the grouping is "not repugnant to scientific classification," or, in other words, belong to a recognized scientific classification. Harnisch, 631 F.2d at 722. Although there is no threshold quanta of structural similarity that is necessary to render the alternative species not repugnant to scientific classification, the shared backbone of a nucleic acid sequence or amino acid sequence can be sufficient (Ren, Appeal No. 2015-004371). In the present application, there is not only a shared backbone of a nucleic acid sequence or amino acid sequence but the PIF transcription factor polypeptides also share a VHNLSERRRRD (SEQ ID NO:113) sequence motif and a phyB-binding domain. Different sequences of an art-recognized class that share a common use may be properly grouped together (Narva, Appeal No. 2018-006168). When considering the whole of the recited polynucleotide and polypeptide sequences claimed, each member of the claimed set of sequences shares the structural feature of being a polynucleotide encoding a PIF transcription factor polypeptide, wherein the PIF transcription factor polypeptide sequence comprises a bHLH domain characterized by the presence of a VHNLSERRRRD (SEQ ID NO:113) sequence motif. Further, each of the members of the claimed group of sequences share a common use that directly flows from this shared structural similarity. In particular, the claimed PIF transcription factor polypeptides share a common function as being transcription factor polypeptides that regulate cell elongation. In view of the forgoing, Applicant submits that the polynucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, 82, 84-87, 88-91, 92-95, 96-108 and 109-112, the polynucleotide sequences of SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, and 135, the polypeptide sequences of SEQ ID NOs:71, 74, 77, 80, and 83, and the polypeptide sequences of SEQ ID NOs:121, 123, 125, 127, and 131 recited in the claims satisfy the requirements for proper Markush groupings as defined by MPEP 2117(II)(A). It is, therefore, respectfully submitted that this rejection should be withdrawn. Examiner’s Response: In view of Applicant’s arguments, the Improper Markush Grouping rejection has been withdrawn. Applicant argues beginning on p. 12 of remarks dated 07/22/2026 the following arguments: III. Rejection under 35 U.S.C. & 112 Claims 1, 10, 13-18, 20 and 33 are rejected under 35 U.S.C. § 112(a) as failing to comply with the written description requirement. See Office Action, page 9. Applicant respectfully requests reconsideration. Without acquiescing to the rejection and in a good faith effort to expedite allowance of the present application, claim 1 is amended herein to recite, in part, that the PIF transcription factor comprises a basic Helix Loop Helix (bHLH) domain comprising the amino acid sequence of SEQ ID NO:113 and the at least one mutation is: (1) an in-frame deletion and/or (2) a mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor. Applicant respectfully submits that the application as filed clearly provides a sufficient description of the invention as claimed. In particular, while the Office Action assert that 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, Applicant submits that the specification and claims provide that the PIF transcription factor comprises a basic Helix Loop Helix (bHLH) domain comprising the amino acid sequence of SEQ ID NO:113 and that the at least one mutation disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof thereby providing a common structure and function to the claimed mutant. Further, the specification discloses the nucleotide and amino acid sequences of five different PIF genes and polypeptides, and further describes orthologs and homologues of the same. In particular, the disclosure at pages 28-34 of the specification teaches that the compositions and methods of the invention comprise homologues including orthologs from the same and from other species. The cited passage goes on to indicate that a homologue of a nucleotide or polypeptide sequence of this invention may share a substantial sequence identity to the nucleotide or protein sequence of the invention, e.g., at least about 80% or 90% sequence identity, and provides various methods for identifying sequences that share substantial sequence identity including inter alia the use of local homology algorithms and hybridization techniques. In particular, at page 34, lines 23- 26, the specification states: "Nucleotide sequences that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This can occur, for example, when a copy of a nucleotide sequence is created using the maximum codon degeneracy permitted by the genetic code." Therefore, considering the homologs and orthologs described in the specification, as well as the codon degeneracy permitted by the genetic code and methods set forth in the specification, Applicant submits that one of ordinary skill in the art could readily envision and routinely identify a nucleotide sequence having at least 80% identity or less to any one of the nucleotide or polypeptide sequences recited in claim 1 or a nucleotide sequence having at least 90% identity or less to any one of the nucleotide or polypeptide sequences recited in claim 20. In addition, the specification and claims disclose functional characteristics that distinguish the sequences of the claimed genus. Specifically, the claims recite that the claimed endogenous gene encodes a Phytochrome Interacting Factor (PIF) transcription factor, which, as is evident from the name, is a transcription factor with promoter binding activity, wherein the at least one mutation in the PIF transcription factor disrupts binding of the PIF transcription factor to DNA in the corn plant or plant part thereof. Therefore, both the structural and functional properties that characterize the genus of sequences that can be used to practice the invention are found in the claims and specification. Accordingly, the specification provides the requisite correlation between the structure of the claimed nucleic acid and protein sequences and the function thereof. See, University of Rochester v. G.D. Searle & Co., 358 F. 3d 916,925 (Fed. Cir. 2004), and Enzo Biochem Inc. v. Gen-Probe Inc., 296 F .3d 1316, 1324 (Fed. Cir. 2002). Moreover, the specification teaches that the plant may be a corn plant and shows that the introduction of at least one mutation in an endogenous PIF gene as claimed results in a corn plant exhibiting a reduced Shade Avoidance Response 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 (SAR) when planted in close proximity with one or more plants. See Specification, Examples 1-4, which disclose mutations in each of Zm00001d040536 (SEQ ID NO:69), Zm00001d033267 (SEQ ID NO:78) and Zm00001d034298 (SEQ ID NO:81) and show that said mutants exhibit reduced SAR. In view of the amount of guidance provided in the present specification, as well as what was known in the art at the time, the skilled artisan would have reasonably concluded, at the time the application was filed, that Applicant had possession of the subject matter claimed. Accordingly, Applicant submits that claims 1, 10, 13-18, 20 and 33 satisfy the written description requirement and respectfully requests the withdrawal of this rejection. Examiner’s Response: Applicant’s argument is not persuasive because there is still at least a lack of adequate written description in the specification of endogenous corn PIF transcription factors that encode polynucleotide or polypeptide sequences with as low as 80% sequence identity to each of the claimed sequences. There is also a dearth of description in the prior art of endogenous corn PIF transcription factor sequences with as low as 80% sequence identity to the claimed sequences, which is evidenced by, for example, the large gap between sequential search results of SEQ ID NO: 80 wherein the next sequence below 91.4% is 67% and not described as a PIF polypeptide nor a sequence from corn. This same reasoning applies to the other claimed polypeptide sequences and all of the claimed nucleotide sequences. Thus, neither the Applicant nor prior art has described these sequences and therefore the ordinary artisan would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed. For this reason, the rejection is maintained. Applicant argues beginning on p. 14 of remarks dated 07/22/2026 the following arguments: IV. Rejection under 35 U.S.C. 4 102 Claims 1, 10, 13-18 and 33 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by Wu (Plant physiology, 181(2), 789-803, 2019; hereinafter "Wu") and as evidenced by maizeGDB GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43, B73 RefGen_v3; hereinafter "maizeGDB"). See Office Action, page 14. Applicant respectfully requests reconsideration. Wu describes the characterization of PIF3.1, PIF3.2, PIF3.3, PIF4.1, PIF4.2, PIF5.1 and PIF5.2 genes in corn. In particular, Wu shows that each of the seven ZmPIF proteins were functional as they complemented the Arabidopsis pifq mutant phenotype; complemented seedling exhibited significantly elongated hypocotyls and partially closed apical hooks compared with pifq. See Wu, pages 793, col. 2, para. 2 to page 794, col. 2 and Figures 5A-F. In addition, consistent with the morphological phenotype, the expression of two genes involved in dark-induced hypocotyl elongation, XTH1S and IAA19, was dramatically elevated in each ZmPIF overexpressing line. See Wu, pages 795, col. 1-2 and Figures 5G-H. Therefore, Wu shows that the polypeptide encoded by the Zmpif4.2 gene (GRMZM2G165042) necessarily binds to DNA because it is shown to exhibit transcription factor activity. Accordingly, while the Office Action asserts that the Zmpif4.2 gene (GRMZM2G165042) has an amino acid sequence that is 99% identical to instant SEQ ID NO:80 as evidenced by maizeGDB (See Office Action, page 17), Applicant submits that the polypeptide encoded by the Zmpif4.2 gene (GRMZM2G165042) is functional and therefore does not comprise at least one mutation that disrupts binding of the PIF transcription factor to DNA in a corn plant or plant part thereof as claimed. The Office Action also asserts that Wu discloses a ZmPIF4.2-KO mutant comprising a 322 bp deletion and a single nucleotide deletion, which would result in an out-of-frame mutation and a polypeptide having the amino acid sequence: MNQFVPDWSNTSRAAGTSQSQQRTTGAAAAGRARCRRGTRAT* (asterisk representing stop codon). See Office Action, page 19. As discussed above, claim 1 is amended herein to recite, in part, that the at least one mutation is: (1) an in-frame deletion and/or (2) a mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor. Applicant submits that the 322 bp deletion/1 bp deletion mutant of Wu is neither an in-frame deletion nor does this mutant remove part, but not all of, the amino acids of SEQ ID NO:113, as claimed. For at least the foregoing reasons, Wu as evidenced by maizeGDB does not anticipate claims 1, 10, 13-18 and 33 under 35 U.S.C. §102(a)(1). Accordingly, Applicant respectfully requests withdrawal of the rejection. Examiner’s Response: In view of the currently amended claims, the previous rejections under 35 USC 102 have been withdrawn. However, in view of Applicant’s amendments, the claims are now rejected under 35 USC 103. Applicant argues beginning on p. 15 of remarks dated 07/22/2026 the following arguments: V. Rejection under 35 U.S.C. & 103 Claim 20 is rejected under 35 U.S.C. § 103 as being unpatentable over Wu and maizeGDB as applied to claim 1, and further in view of Li (Small Methods, 3(3), 1800473, 2019; hereinafter "Li") and GenBank accession No. DAA50359 (putative HLH DNA-binding domain superfamily protein; hereinafter "DAA50359"). See Office Action, page 20. Applicant respectfully requests reconsideration. Claim 1, upon which claim 20 depends, is amended herein to recite that the at least one mutation is: (1) an in-frame deletion and/or (2) a mutation that removes part, but not all of, the amino acids of SEQ ID NO:113 from the PIF transcription factor. As discussed above, the 322 bp deletion/1 bp deletion mutant of Wu is neither an in-frame deletion nor does this mutant remove part, but not all of, the amino acids of SEQ ID NO:113, as claimed. In addition, nowhere does the combination of Wu and maizeGDB in view of Li and DAA50359 teach or suggest any one of the specific mutant nucleotide sequences of SEQ ID NOs:120, 122, 124, 126, 128, 129, 130, 132, 133, 134, or 135 or mutated PIF polypeptide sequences of SEQ ID NOs:121, 123, 125, 127, or 131, as claimed. The endogenous PIF gene sequences of SEQ ID NOs:69, 72, 75, 78 and 81 are 7422, 7354, 6534, 16789, and 7960 nucleotides in length, respectively. Applicant submits that there are a multitude of possible mutations that could be made in any one of these sequences and considerable trial and error experimentation would be required to arrive at the recited sequences and without a reasonable expectation of success. Further, assuming for the sake of argument that the ordinarily skilled artisan was seeking to reduce SAR in corn, Wu suggests that ZmPIF3s, and not PIF4.2, are the dominant positive regulators of early shade response in maize. See Wu, page 797, col. 2, para. 1. Therefore, there would have been no motivation or reasonable expectation that deleting the 22 amino acid residues from the polypeptide sequence of SEQ ID NO:80, as in SEQ ID NO:125, would have successfully reduced a shade avoidance response in maize as the Office Action contends. In view of the foregoing, Applicant submits that the combination of Wu, maizeGDB, Li and DAA50359 fails to make the claimed invention obvious for at least the reasons that the cited references fail to teach or suggest all of the elements of the claims and fails to provide a reasonable expectation of success in achieving the presently claimed invention. Accordingly, Applicant respectfully requests that this rejection be reconsidered and withdrawn. Examiner’s Response: In view of Applicant’s amendments, a modified rejection under 35 USC 103 has been made to the claims. The bHLH domain of which the PIF polypeptide of SEQ ID NO: 80 is defined by (see title of GenBank Accession No. DAA50359 which is linked to the maizeGDB GRMZM2G165042 sequence) was clearly annotated at the time of filing, and would have been understood by the ordinary artisan to be essential to the function of the polypeptide. It would be obvious to delete or mutate any residue in this known bHLH domain for the purpose of disrupting PIF function with a reasonable expectation of success. Additionally, although Wu suggests that ZmPIF3s, and not PIF4.2, are the dominant positive regulators of early shade response in maize, Wu also clearly teaches plants comprising a knockout of of ZmPIF3, ZmPIF4, or ZmPIF5 were all less responsive to shade treatment (abstract, and p. 799, left column). Because ZmPIF4 does contribute to shade avoidance response as taught by Wu, the ordinary artisan would in fact be motivated to delete regions of the bHLH domain including the 22 amino acid residues from the polypeptide sequence of SEQ ID NO:80, as in SEQ ID NO:125, and have a reasonable expectation of success of conferring a maize plant with a modulated shade avoidance response. For these reasons, Applicant’s argument is not persuasive. Applicant argues beginning on p. 16 of remarks dated 07/22/2026 the following arguments: VI. Double Patenting Rejections A. 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. 18/664,349. See Office Action, page 24. Applicant respectfully requests reconsideration. Claim 54 is not pending in this application and claims 55 and 64 are withdrawn by the Examiner as being directed to a non-elected invention and are not currently under examination. For at least these reasons, withdrawal of this rejection is respectfully requested. B. 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. 18/664,349 in view of Wu and as evidenced by maizeGDB. See Office Action, page 25. 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. 18/664,349 in view of Wu and maizeGDB as applied previously herein, and further in view of Li and DAA50359. See Office Action, page 31. As the Examiner has acknowledged, these are provisional rejections because the claims of the co-pending application have not been patented. Applicant respectfully requests the rejections be held in abeyance on this basis. Examiner’s Response: The rejection to claim 54 is withdrawn because this claim is cancelled. Claims 55 and 64 are still pending, and therefore the rejection to these claims is maintained. The provisional rejection is also maintained because the rejection remains applicable. Conclusion and Inquiries No claims are allowed. THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to 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. 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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