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 Claims
The amendments submitted on May 5th, 2026 have been entered.
Claims 1-49, 52, 56-58, 60-62, 66-68, and 70-113 have been canceled.
New claims 114-116 have been added.
Claims 50-51, 53-55, 59, 63-65, 69, and 114-116 are pending in the application.
Claims 50-51, 53-55, 59, 63-65, 69, and 114-116 are examined in this Office action.
The text of those sections of Title 35 U.S. Code, not included in this action, can be found in a prior Office action.
Withdrawn Objections and Rejections
The rejection of claims 50-51, 53-55, 59, 63-65, and 69 under 35 USC § 112(b) for indefiniteness is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claims 50-51, 53-55, 59, 63-65, and 69 under 35 USC § 112(a) for lack of written description is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claims 50-51, 53-55, 59, 63-65, and 69 under 35 USC § 102 is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claims 50-51, 53-55, 59, 63-65, and 69 under 35 USC § 101 (double patenting) is withdrawn in light of Applicant’s amendments to the claims.
New Rejections
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 50-51, 53-55, 59, 63-65, 69, and 114-116 are rejected under 35 U.S.C. 103 as being unpatentable over Allen, E. et al., “Methods and Compositions for Short Stature Plants Through Manipulation of Gibberellin Metabolism to Increase Harvestable Yield,” US Patent Application Publication No. US 20180051295 A1, filed August 17th, 2017, published February 22nd, 2018 (see, IDS 4/4 filed 05/09/2025 and IDS filed 08/16/2024), in view of Wu, W. et al. US Patent Publication No. US 20140359836 A1, “Isolated Novel Nucleic Acid and Protein Molecules from Corn and Methods of Using Those Molecules to Generate Transgenic Plant with Enhanced Traits”, published 01/19/2012. This is a new rejection necessitated by the claim amendments.
The applied Allen reference has a common inventor, Slewinski, T. and common assignee, Monsanto, with the instant application. Based upon the earlier publication date of the reference, it constitutes prior art and does not qualify for an exception.
Claim 50 recites a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the guide RNA comprises a guide sequence that is at least 95% identical or complementary to at least 17 consecutive nucleotides of a target DNA sequence within a genomic locus of an endogenous GA3 oxidase gene of a corn or cereal plant, wherein the GA3 oxidase gene encodes a protein that comprises an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:173.
Claim 51 recites the recombinant DNA construct of claim 50, wherein the target DNA sequence comprises the nucleotide sequence of SEQ ID NO: 170.
Claim 53 recites a composition comprising the recombinant DNA construct of claim 50, further comprising an RNA-guided endonuclease.
Claim 54 recites the composition of claim 53, wherein the RNA-guided endonuclease in the presence of the guide RNA molecule causes a double strand break or nick at or near the target DNA sequence in a genome of the corn or cereal plant.
Claim 55 recites a composition comprising the recombinant DNA construct of claim 50, further comprising a recombinant DNA donor template comprising at least one homology sequence or homology arm, wherein the at least one homology sequence or homology arm is at least 70% complementary to at least 20 consecutive nucleotides of the target DNA sequence
Claim 59 recites the recombinant DNA construct of claim 50, wherein: a) the transcribable DNA sequence is operably linked to a plant-expressible promoter.
Claim 63 recites a DNA molecule or vector comprising the recombinant DNA construct of claim 50.
Claim 64 recites a bacterial or host cell comprising the recombinant DNA construct of claim 50.
Claim 65 recites a corn or cereal plant, plant part or plant cell comprising the recombinant DNA construct of claim 50.
Claim 69 recites a composition comprising a first DNA molecule or vector and a second DNA molecule or vector, wherein the first DNA molecule or vector comprises the recombinant DNA construct of claim 50, and the second DNA molecule or vector comprises: a) a second recombinant DNA construct encoding an RNA-guided endonuclease.
Claim 114 recites the recombinant DNA construct of claim 50, wherein the target DNA sequence comprises a coding sequence comprising the nucleotide sequence of SEQ ID NO: 172.
Claim 115 recites the recombinant DNA construct of claim 50, wherein the target DNA sequence comprises the exonic nucleotide sequences of SEQ ID NO:171.
Claim 116 recites the recombinant DNA construct of claim 50, wherein the GA3 oxidase gene encodes a protein that comprises the amino acid sequence of SEQ ID NO: 173.
Regarding claims 50 and 116, Allen teaches compositions and methods for altering gibberellin (GA) content in corn or other cereal plants [Abstract]. Methods and compositions are provided for altering the expression of genes related to gibberellin biosynthesis through suppression, mutagenesis and/or editing of GA20 or GA3 oxidase genes. Allen teaches that manipulation of GA levels in various agriculturally important crops, such as semi-dwarf wheat, rice, and sorghum, led to increased yield and reduced lodging, but that manipulation of the GA pathway in corn has been associated with off-types that are incompatible to yield [¶04]. Allen further teaches that the modified corn and cereal crop plants of the invention have reduced gibberellin levels and improved characteristics, such as reduced plant height and increased lodging resistance with less off-types, but indicates that there continues to be a need in the art for the development of such plants [Abstract; ¶04].
Allen teaches Embodiment 165, wherein a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the guide RNA molecule comprises a guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a target DNA sequence at the genomic locus of an endogenous GA oxidase gene of a corn or cereal plant (i.e., a recombinant DNA construct comprising transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the guide RNA comprises a guide sequence that is at least 95% identical or complementary to at least 17 consecutive nucleotides of a target sequence within a genomic locus) [¶390]. Allen teaches that plants or plant cells may be transformed with a transcribable DNA sequence encoding a non-coding RNA molecule that targets at least one GA20 oxidase gene and/or at least one GA3 oxidase gene for suppression (i.e., endogenous GA3 oxidase gene) [¶211].
Allen does not explicitly teach the recombinant DNA construct wherein the GA3 oxidase gene encodes a protein that comprises an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO: 173. However, Wu teaches nucleic acids and polypeptides, as well as transgenic plants, seeds, cells containing DNA for expression of the proteins that are useful for imparting enhanced agronomic traits linked to transgenic crop plants, particularly corn plants [Abstract; ¶02]. Wu teaches recombinant DNA constructs having polynucleotides characterized by reference to SEQ ID NO:1-41779 and the cognate proteins with amino acid sequences having reference to SEQ ID NO:41780-83558 used to provide enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells [¶04]. Wu teaches that the enhanced traits include increased yield in corn [¶06].
Wu teaches SEQ ID NO: 46179 with 100% identity to SEQ ID NO: 173 of the instant application (see alignment below). This protein is characterized as a putative 2-oxoglutarate-dependent dioxygenase in the 2OG -Fe(II) oxygenase superfamily (see sequence features below). It is known in the art that GA20 and GA3 oxidase genes fall within the 2–oxoglutarate-dependent dioxygenase superfamily1. Based on the sequence identity, the characterization and the function of the disclosed protein, this is taken to read on the GA3 oxidase gene encoding a protein with 95% identity to the amino acid sequence of SEQ ID NO: 173 of the instant application.
ALIGNMENT:
Query Match 100.0%; Score 1669; Length 317;
Best Local Similarity 100.0%;
Matches 317; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEIATVDLRGVVPGGAGWEAARAAVTASMVAHGCVVVAHDAVGADLRQALFSRALPELFA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEIATVDLRGVVPGGAGWEAARAAVTASMVAHGCVVVAHDAVGADLRQALFSRALPELFA 60
Qy 61 LPLEAKQRTVSPNGEFRGYIGQRPGMDWESLRVGKPTDAASVSGFAETLWPEGNPEFCDT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LPLEAKQRTVSPNGEFRGYIGQRPGMDWESLRVGKPTDAASVSGFAETLWPEGNPEFCDT 120
Qy 121 IVAFAENMMELEGTVETLVLEGLGARGQSIRAHFGSLDHAVRLSHYGVPPDTESSMSMQP 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 IVAFAENMMELEGTVETLVLEGLGARGQSIRAHFGSLDHAVRLSHYGVPPDTESSMSMQP 180
Qy 181 HYDDSVVTAIVQHEVEGLEMHAGDGRWVAVPAEVGTLTFVAGEQFRVVTNGRVPACLHRV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HYDDSVVTAIVQHEVEGLEMHAGDGRWVAVPAEVGTLTFVAGEQFRVVTNGRVPACLHRV 240
Qy 241 RTPSNRERFSVLFGRRQKDGVAVRAMEDLVDAEHPLAYNPLRHEEYSRWRVTPGFRRQTE 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 RTPSNRERFSVLFGRRQKDGVAVRAMEDLVDAEHPLAYNPLRHEEYSRWRVTPGFRRQTE 300
Qy 301 CEPCTCQDQLFTYTAVT 317
|||||||||||||||||
Db 301 CEPCTCQDQLFTYTAVT 317
PNG
media_image1.png
818
848
media_image1.png
Greyscale
The skilled artisan would have expected success in substituting a gene encoding SEQ ID NO: 46179 of Wu for the GA20 and/or GA3 oxidase because Allen teaches that targeting at least one GA20 and/or GA3 oxidase gene for suppression enhances yield and lodging resistance and Wu teaches that SEQ ID NO: 46179 is characterized as a putative 2-oxoglutarate-dependent dioxygenase in the 2OG -Fe(II) oxygenase superfamily. The skilled artisan could have substituted one gene for the other because Wu teaches that the genes and proteins aid in enhancing agricultural traits in corn, such as yield, the trait that Allen suggests is often decreased by GA biosynthesis modification off-types. One of ordinary skill in the art at the time of filing would have found it obvious to make the substitution because both Allen and Wu provide methodology for incorporating such a gene and encoded protein into a recombinant DNA construct for enhancing agricultural traits in corn. Thus, one would have reasonable expectation of success in the substitution aiding in enhanced yield and other characteristics such as lodging resistance, as taught by Allen. A person of ordinary skill in the art would have been motivated to use the SEQ ID NO: 46179 of Wu, a putative 2-oxoglutarate-dependent dioxygenase in the 2OG -Fe(II) oxygenase superfamily, because Allen teaches that GA3 and GA20 oxidases have had improved lodging resistance in corn, but without off-types, when suppressed or when activity or expression is reduced.
Regarding claim 51 and 115, Allen teaches that methods and techniques for designing targeting constructs and guide RNAs for genome editing and site-directed integration at a target site within the genome of a plant are known in the art, and further teaches guide RNAs targeting GA oxidase genes for suppression [¶171; 395; 515]. Allen teaches that a “target site” for genome editing refers to the location of a polynucleotide sequence within a plant genome that is bound and cleaved by a site-specific nuclease introducing a double stranded break (or single-stranded nick) into the nucleic acid backbone of the polynucleotide sequence and/or its complementary DNA strand [¶59]. A “target site” for an RNA-guided nuclease may comprise the sequence of either complementary strand of a double-stranded nucleic acid (DNA) molecule or chromosome at the target site. The guide RNA comprises a guide or targeting sequence that is identical or complementary to a target site within the plant genome, such as at or near a GA oxidase gene, but that perfect identity or complementarity may not be required for a non-coding guide RNA to bind or hybridize to a target site. [¶59; 160].
Wu additionally teaches that recombinant DNA constructs can be designed to suppress the level of an endogenous protein, wherein the suppression occurs through matching the DNA to a targeted gene. Wu further teaches SEQ ID NO: 4400, the polynucleotide cognate to the peptide SEQ ID NO: 46179 shown above. It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to design a targeting construct as taught by Allen for the guide RNA to target the GA3 oxidase gene of Wu for suppression of GA oxidase genes because Allen teaches that the design of such target DNA sequences for guide RNA are known in the art and essential for suppression of gibberellin biosynthesis-related genes. One would be motivated to use a target sequence comprising a portion of SEQ ID NO: 4400 to alter the activity of SEQ ID NO: 46179 for improved characteristics in corn such as yield, lodging resistance, and reduced plant height. One would have reasonable expectation of success as Allen teaches that the guide RNA may be complementary or identical and need not be an exact match to the target sequence for the guide RNA to bind or hybridize to the target site. Additionally, Allen teaches guide RNAs targeting GA20 and GA3 oxidase genes for suppression, as such it would be obvious to simply substitute SEQ ID NO: 4400 of Wu to achieve the same predicted result.
SEQ ID NO: 4400 comprises 13% identity to SEQ ID NO: 170 of the instant application (see alignment below), which is sufficient to read on the guide RNA target at least 95% identity to at least 17 consecutive nucleotides of the target sequence within a genomic locus of an endogenous GA3 oxidase gene of a corn plant, as claimed in the instant application.
Alignment statistics for match #1
NW Score
Identities
Gaps
Strand
-11822
954/7332(13%)
6378/7332(86%)
Plus/Plus
Query 3121 GGCGCGAGGCATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGG 3180
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 ----------ATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGG 50
Query 3181 GTGGGAGGCCGCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGT 3240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 51 GTGGGAGGCCGCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGT 110
Query 3241 GGCGCACGACGCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGA 3300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 111 GGCGCACGACGCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGA 170
Query 3301 GCTCTTCGCGCTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAG 3360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 171 GCTCTTCGCGCTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAG 230
Query 3361 GGGCTACATCGGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCAC 3420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 231 GGGCTACATCGGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCAC 290
Query 3421 GGACGCCGCCAGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTT 3480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 291 GGACGCCGCCAGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTT 350
Query 3481 CTGGTGACCCATCCTTCCTTCCTTGGCCACCTTTGAATCTAACTGGCTGCCATCTTTAGT 3540
|||
Sbjct 351 CTG--------------------------------------------------------- 353
Query 3541 TCTTCTGTTCGATTGCTGATCTAACTGGCCACGCACGCGCAGTGACACGATCGTGGCGTT 3600
||||||||||||||||||
Sbjct 354 ------------------------------------------TGACACGATCGTGGCGTT 371
Query 3601 CGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTGGAAGGCCTCGG 3660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 372 CGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTGGAAGGCCTCGG 431
Query 3661 CGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCCGTCCGGCTGTC 3720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 432 CGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCCGTCCGGCTGTC 491
Query 3721 GCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCGCACTACGACGA 3780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 492 GCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCGCACTACGACGA 551
Query 3781 CAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATGCACGCCGGGGA 3840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 552 CAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATGCACGCCGGGGA 611
Query 3841 CGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTCGCCGGCGAGCA 3900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 612 CGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTCGCCGGCGAGCA 671
Query 3901 GTTCAGGGTACGAGCACGGTCCGATCCGATTGACTCCTCTCCCTGAATCCTGACGGTGAC 3960
|||||||||
Sbjct 672 GTTCAGGGT--------------------------------------------------- 680
Query 3961 CAGCCATATATATTGACATTGCCGCTGCGTACGTGCAGGTCGTGACGAACGGGCGCGTGC 4020
||||||||||||||||||||
Sbjct 681 ----------------------------------------CGTGACGAACGGGCGCGTGC 700
Query 4021 CGGCGTGCCTCCACCGCGTGAGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCG 4080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 701 CGGCGTGCCTCCACCGCGTGAGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCG 760
Query 4081 GCCGCCGGCAGAAGGACGGCGTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGC 4140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 761 GCCGCCGGCAGAAGGACGGCGTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGC 820
Query 4141 ACCCGCTGGCGTACAACCCGCTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCG 4200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 821 ACCCGCTGGCGTACAACCCGCTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCG 880
Query 4201 GTTTTAGAAGGCAAACCGAATGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACA 4260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 881 GTTTTAGAAGGCAAACCGAATGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACA 940
Query 4261 CAGCAGTTACATAATATGGACATCATCACACAGTGCTCAAAATAGTATTAAAAGGGGAAA 4320
||||||||||||||
Sbjct 941 CAGCAGTTACATAA---------------------------------------------- 954
Further, SEQ ID NO: 4400 is an 83.5% match to SEQ ID NO: 171 of the instant application, with 100% best local similarity across the entirety of the length of SEQ ID NO: 4400 (954 nucleotides) (see alignment below). Wu teaches that a non-coding RNA molecule may target an intron sequence of a GA oxidase gene instead of, or in addition to, an exonic, 5' UTR or 3' UTR of the GA oxidase gene [¶115]. Thus, the target DNA sequence is interpreted to comprise the exonic nucleotide sequences of SEQ ID NO: 171, and may be used for designing the target DNA sequence in the recombinant DNA construct, absent evidence to the contrary.
Query Match 83.5%; Score 954; Length 954;
Best Local Similarity 100.0%;
Matches 954; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 131 ATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGGGTGGGAGGCC 190
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGGGTGGGAGGCC 60
Qy 191 GCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGTGGCGCACGAC 250
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGTGGCGCACGAC 120
Qy 251 GCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGAGCTCTTCGCG 310
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGAGCTCTTCGCG 180
Qy 311 CTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAGGGGCTACATC 370
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAGGGGCTACATC 240
Qy 371 GGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCACGGACGCCGCC 430
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCACGGACGCCGCC 300
Qy 431 AGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTTCTGTGACACG 490
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 AGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTTCTGTGACACG 360
Qy 491 ATCGTGGCGTTCGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTG 550
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ATCGTGGCGTTCGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTG 420
Qy 551 GAAGGCCTCGGCGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCC 610
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GAAGGCCTCGGCGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCC 480
Qy 611 GTCCGGCTGTCGCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCG 670
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GTCCGGCTGTCGCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCG 540
Qy 671 CACTACGACGACAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATG 730
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CACTACGACGACAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATG 600
Qy 731 CACGCCGGGGACGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTC 790
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CACGCCGGGGACGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTC 660
Qy 791 GCCGGCGAGCAGTTCAGGGTCGTGACGAACGGGCGCGTGCCGGCGTGCCTCCACCGCGTG 850
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GCCGGCGAGCAGTTCAGGGTCGTGACGAACGGGCGCGTGCCGGCGTGCCTCCACCGCGTG 720
Qy 851 AGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCGGCCGCCGGCAGAAGGACGGC 910
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 AGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCGGCCGCCGGCAGAAGGACGGC 780
Qy 911 GTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGCACCCGCTGGCGTACAACCCG 970
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 GTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGCACCCGCTGGCGTACAACCCG 840
Qy 971 CTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCGGTTTTAGAAGGCAAACCGAA 1030
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 CTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCGGTTTTAGAAGGCAAACCGAA 900
Qy 1031 TGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACACAGCAGTTACATAA 1084
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 TGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACACAGCAGTTACATAA 954
Regarding claim 53, Allen teaches a composition comprising the recombinant DNA construct of Embodiment 165, a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the guide RNA molecule comprises a guide sequence that is at least 95% complementary to at least 17 consecutive nucleotides of a target DNA sequence at or near the genomic locus of an endogenous GA oxidase gene of a corn or cereal plant [¶390; 402] and further comprising a RNA-guided endonuclease [¶403].
Regarding claim 54, Allen teaches the composition comprising Embodiment 165, wherein an engineered site-specific nuclease that binds to a target site at the genomic locus of an endogenous GA oxidase gene of a corn or cereal plant and causes a double-strand break or nick at the target site [¶424].
Regarding claim 55, Allen teaches a composition comprising the recombinant DNA construct of Embodiment 165 [¶402] and further comprising a recombinant DNA donor template comprising at least one homology sequence or homology arm, wherein the at least one homology sequence or homology arm is at least 70% complementary to at least 20 consecutive nucleotides of a target DNA sequence [¶408].
Allen teaches that a "donor template" which may be a recombinant DNA donor template, is defined as a nucleic acid molecule having a nucleic acid template or insertion sequence for site-directed, targeted insertion or recombination into the genome of a plant cell via repair of a nick or double-stranded DNA break in the genome of a plant cell [¶60]. Allen teaches that a donor template must have at least one homology arm or homology sequence to direct the integration of a mutation or insertion sequence. Allen teaches that the homology sequence or homology arm(s) are identical or complementary, or have a percent identity or percent complementarity, to a sequence at a target site within the genome of a plant, such as at or near a GA3 oxidase or GA20 oxidase gene within the genome of a plant. [¶61-62]. Allen further provides embodiments including recombinant DNA donor template comprising at least one homology sequence identical or complementary to a portion of specific GA3 and GA20 oxidase sequences [¶412].
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to include a recombinant DNA donor template comprising at least one homology sequence or homology arm to provide the necessary information for insertion or alteration of a gene. One of ordinary skill in the art would use the target DNA sequence within a genomic locus of an endogenous GA3 oxidase gene to ensure proper targeting for insertion or repair of a DNA nick or break in the genome of the plant cell to achieve the desired effect of improved agronomic traits. One would have reasonable expectation of success in creating a composition comprising the recombinant DNA construct comprising a recombinant DNA donor template comprising at least one homology arm or sequence with at least 70% complementary to at least 20 consecutive nucleotides of the target DNA sequence because Allen already teaches and demonstrates such compositions with other GA oxidase genes.
Regarding claim 59, Allen teaches the recombinant DNA construct of Embodiment 165, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter [¶393].
Regarding claim 63, Allen teaches a DNA molecule comprising the recombinant DNA construct of Embodiment 165 [¶398].
Regarding claim 64, Allen teaches a bacterial cell comprising the recombinant DNA construct of Embodiment 165 [¶400].
Regarding claim 65, Allen teaches a corn or cereal plant, plant part or plant cell comprising the recombinant DNA construct of Embodiment 165 [¶401].
Regarding claim 69, Allen teaches a composition comprising the recombinant DNA construct of Embodiment 165, comprising a first DNA molecule or vector and a second DNA molecule or vector, wherein the first DNA molecule or vector comprises the recombinant DNA construct encoding the guide RNA molecule, and the second DNA molecule or vector comprises the second recombinant DNA construct encoding the RNA-guided endonuclease [¶407].
Regarding claim 114, as detailed above, Wu teaches SEQ ID NO: 4400, the polynucleotide cognate of SEQ ID NO: 46179. SEQ ID NO: 4400 has 100% identity to SEQ ID NO: 172 of the instant application (see alignment below). According to the rationale above, it would have been prima facie obvious to one of ordinary skill in the art at the time of filing to design a targeting construct as taught by Allen for the guide RNA to target the GA3 oxidase gene (SEQ ID NO: 4400) of Wu for suppression of GA oxidase genes because Allen teaches that the design of such target DNA sequences for guide RNA are known in the art and essential for suppression of gibberellin biosynthesis-related genes. One would be motivated to use a target sequence comprising a portion of SEQ ID NO: 4400 to suppress activity of SEQ ID NO: 46179 for improved characteristics in corn such as yield, lodging resistance, and reduced plant height. One would have reasonable expectation of success as Allen teaches that the guide RNA may be complementary or identical and need not be an exact match to the target sequence for the guide RNA to bind or hybridize to the target site. Additionally, Allen teaches guide RNAs targeting GA20 and GA3 oxidase genes for suppression and that such designing is known in the art. As such, it would be obvious to simply substitute SEQ ID NO: 4400 of Wu to achieve the same predicted result. As it is a 100% match for SEQ ID NO: 172 of the instant application, the target DNA sequence would inherently comprise a coding sequence comprising the nucleotide sequence of SEQ ID NO: 172.
Query Match 100.0%; Score 954; Length 954;
Best Local Similarity 100.0%;
Matches 954; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGGGTGGGAGGCC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGAGATCGCGACGGTTGACCTCCGCGGGGTGGTGCCGGGGGGCGCCGGGTGGGAGGCC 60
Qy 61 GCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGTGGCGCACGAC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GCCCGCGCGGCGGTGACCGCGTCCATGGTGGCGCACGGCTGCGTCGTCGTGGCGCACGAC 120
Qy 121 GCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGAGCTCTTCGCG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GCGGTCGGCGCGGACCTCCGGCAGGCGCTGTTCTCCCGCGCGCTGCCGGAGCTCTTCGCG 180
Qy 181 CTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAGGGGCTACATC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 CTCCCTCTCGAGGCCAAGCAGCGGACGGTGTCGCCCAATGGGGAGTTCAGGGGCTACATC 240
Qy 241 GGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCACGGACGCCGCC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GGCCAGCGCCCCGGCATGGACTGGGAGAGCCTCCGCGTCGGAAAGCCCACGGACGCCGCC 300
Qy 301 AGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTTCTGTGACACG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 AGCGTCAGCGGCTTCGCTGAGACGCTCTGGCCGGAGGGAAACCCAGAGTTCTGTGACACG 360
Qy 361 ATCGTGGCGTTCGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ATCGTGGCGTTCGCCGAGAACATGATGGAGCTGGAGGGGACGGTGGAGACGCTGGTCCTG 420
Qy 421 GAAGGCCTCGGCGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GAAGGCCTCGGCGCCCGCGGGCAGAGCATCCGCGCCCACTTCGGCTCGCTCGACCACGCC 480
Qy 481 GTCCGGCTGTCGCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GTCCGGCTGTCGCACTACGGCGTGCCGCCGGACACGGAGAGCAGCATGTCGATGCAGCCG 540
Qy 541 CACTACGACGACAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATG 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CACTACGACGACAGCGTGGTGACCGCGATCGTGCAGCACGAGGTGGAAGGGCTCGAGATG 600
Qy 601 CACGCCGGGGACGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTC 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CACGCCGGGGACGGGCGCTGGGTCGCCGTCCCTGCCGAAGTCGGCACCCTCACCTTCGTC 660
Qy 661 GCCGGCGAGCAGTTCAGGGTCGTGACGAACGGGCGCGTGCCGGCGTGCCTCCACCGCGTG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GCCGGCGAGCAGTTCAGGGTCGTGACGAACGGGCGCGTGCCGGCGTGCCTCCACCGCGTG 720
Qy 721 AGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCGGCCGCCGGCAGAAGGACGGC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 AGGACGCCCAGCAACCGCGAGCGGTTCTCGGTGCTGTTCGGCCGCCGGCAGAAGGACGGC 780
Qy 781 GTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGCACCCGCTGGCGTACAACCCG 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 GTGGCGGTGCGCGCGATGGAGGACCTCGTCGACGCGGAGCACCCGCTGGCGTACAACCCG 840
Qy 841 CTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCGGTTTTAGAAGGCAAACCGAA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 CTGCGCCATGAGGAGTACTCCAGGTGGCGTGTCACACCCGGTTTTAGAAGGCAAACCGAA 900
Qy 901 TGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACACAGCAGTTACATAA 954
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 TGCGAACCATGTACGTGCCAGGATCAGTTATTCACGTACACAGCAGTTACATAA 954
Examiner’s Note
Examiner notes that Application No. 18/713,008 with a common Applicant has overlapping subject material. Most notably, a non-coding guide RNA molecule comprising a sequence that is at least 80% complementary to at least 15 consecutive nucleotides of a /mRNA molecule encoding an endogenous GA oxidase protein, the GA oxidase protein being at least 80% identical to SEQ ID NO: 89, which had 100% identity to SEQ ID NO: 173 of the instant application. However, in Application No. 18/713,008, in the Response to Restriction and Election of Species Requirement filed March 4th, 2026, the Applicant elected the species (i), a mutant allele of an endogenous brachytic 2 (br2) gene. Thus, with regard to the species election, a non-statutory double patenting rejection is not being considered.
Response to Applicant’s Arguments
The Applicant’s arguments filed May 5th, 2026, with respect to the rejection of claims 50-51, 53-55, 59, and 69 under 35 USC § 112(a), 102, and 101 have been carefully considered but are moot in light of Applicant’s amendments to the claims.
Summary
Claims 50-51, 53-55, 59, 63-65, 69, and 114-116 are rejected.
Applicants’ amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR § 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY K. JOHNSON whose telephone number is (571)272-5761. The examiner can normally be reached Monday - Friday 7:30 am - 5:00 pm.
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/EMILY K JOHNSON/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Hu, L. et al. (2021, “Gibberellin Oxidase Gene Family in L. chinense: Genome-Wide
Identification and Gene Expression Analysis”, Int. Jour. of Mol. Sci. 22, 7167,
https://doi.org/10.3390/ijms22137167) teaches that GAox belongs to the 2OG-Fe (II) oxygenase superfamily, which is divided into multiple small families based on structural and functional differences [pg. 2, ¶1]. The GA20ox, GA2ox, and GA3ox gene families play an important role in GA biosynthesis and degradation. The GA20ox, GA2ox, and GA3ox genes belong to the 2–oxoglutarate-dependent dioxygenase superfamily in plants and play an important role in the final step of GA biosynthesis [pg. 2, ¶3].
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