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 received on 05/20/2026 have been entered. Claims 66, 69-70, 76, 78, 87-88, and 118-130 are pending.
Claims 66, 69-70, 76, 78, and 87 remain withdrawn for being directed to a non-elected invention(s).
Claims 88 and 118-130 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.
Claim Rejections - 35 USC § 103
Claims 88 and 118-130 remain rejected under 35 U.S.C. 103 as being unpatentable over Youssef (Youssef et al., 2017, Nature Genetics, Vol. 49(1), pp. 157-161; included on IDS dated 03/14/2023). All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim.
Claim 88 recites “[a] guide nucleic acid that binds to a target site in a corn Short Internodes (SHI) transcription factor gene that encodes a SHI transcription factor, wherein the SHI transcription factor is a SIX-ROWED SPIKE 2 (VRS2) transcription factor, and wherein the target site encodes a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:88-92”.
Youssef teaches the Six-rowed spike 2 (Vrs2), which encodes a SHORT INTERNODES (SHI) transcriptional regulator (i.e., a Short Internodes (SHI) transcription factor gene that encodes a SHI transcription factor, wherein the SHI transcription factor is a SIX-ROWED SPIKE 2 (VRS2) transcription factor) (Youssef, Abstract). Youssef teaches the SHI protein encoded by Vrs2 features two N-terminal zinc-finger-like motifs (CCCH) with a nuclear localization signal (KRRER) and the C-terminal SHI-family-specific IGGH domain (see sequence comparisons below) (Youssef, page 159, right column, last paragraph; Supplementary Figure 3).
Youssef teaches that based on the IGGH domain, 111 SHI-related proteins were identified, including 6 in the barley genome, 4 in Brachypodium distachyon, 6 in rice (Oryza sativa L.), 5 in Sorghum bicolor and 10 in maize (Zea mays L.) (i.e., a corn Short Internodes (SHI) transcription factor gene that encodes a SHI transcription factor) (Youssef, page 159, right column, last paragraph; Supplementary Figure 4).
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The alignment shows the double-CCCH motif (red stars), the nuclear localization signal (KRRER), the IGGH domain (isoleucineglycine-glycine-histidine sequence) (the recited motifs are in bold in the instant sequence below).
INSTANT SEQUENCE SEQ ID NO: 71(instant sequence SEQ ID NO: 88 in box):
MAGFPLGGGSHTQSRDAPASSVPPVHPSDAASFLYAARAGAGLQLWQQQQQHPFYTSNIIRFSDDPPGPAPSLTGATSPSHRTRASGGSGGGGGVSCQDCGNQAKKDCVHQRCRTCCKSRGFACSTHVKSTWVSAAKRRERQQQLAALAASAGDTAAAAGPSRDPTKRPRARLSVVTPTTTSSGDQQMVTVAERFPREVSSEALFRCVRLGPVDRAEAEVAYQTTVSIGGHVFKGLLHDVGPRSLPAAGGGAAAAAIEYYFRHAADGSPPSTTGAAGEACGAGGVGNVVVSSAVVMDPYPTPGSYAAFLPGAPFFPGGHPRQ
Youssef teaches sequence A0A1I9RHG9_HORVU (UniProt) which shares 96.8% sequence identity with instant sequence SEQ ID NO: 88 (i.e., wherein the target site encodes a sequence having at least 80% sequence identity to SEQ ID NO: 88) (see sequence alignment below).
Qy 1 CQDCGNQAKKDCVHQRCRTCCKSRGFACSTH 31
|||||||||||| ||||||||||||||||||
Db 106 CQDCGNQAKKDCQHQRCRTCCKSRGFACSTH 136
It is noted that instant sequence SEQ ID NO: 71 also comprises instant sequences SEQ ID NO: 90 (100% sequence identity to instant sequence SEQ ID NO: 71; instant claim 123); SEQ ID NO: 91 (87.8% sequence identity to instant sequence SEQ ID NO: 71; instant claim 120); and SEQ ID NO: 92 (100% sequence identity to instant sequence SEQ ID NO: 71; instant claim 120).
Youssef teaches mutant barley plants carrying the vrs2.e allele, which comprises an X-ray induced mutation resulting in a single-base-pair deletion at nucleotide position 527 in the first exon resulting in a frameshift mutation (Youssef, page 159, right column, first paragraph; Supplementary Note Table 1).
Additionally, Youssef teaches mutants int-b.3 (deletion identical to that in vrs2.e allele), int-b.6 (a 13-bp deletion in exon 1), and HOR 19366 (a single-base-pair deletion at nucleotide position 504), all of which produce the same premature stop codon (see figure below). In the absence of evidence to the contrary, the deletions taught by Youssef, which introduce a premature stop codon, are capable of disrupting the binding of the SHI family transcription factor to DNA.
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It is noted that it is the position of this Office that any mutation introduced using any guide system in any gene location that disrupts the binding of DNA is rendered obvious by the teachings of Youssef. Although Youssef does not explicitly teach introducing a mutation using an editing system that comprises a guide nucleic acid, there is no way to distinguish a corn plant comprising a mutation introduced using an editing system that comprises a guide nucleic acid from a corn plant comprising a mutation introduced via X-ray, for example. As such, it would have been obvious to one of ordinary skill in the art to introduce a mutation in the location of the VRS2 gene as taught by Youssef to disrupt DNA binding.
At the time the instant application was filed, it would have been obvious and within the scope of one of ordinary skill in the art to utilize the known SHI transcription factor gene from barley as taught by Youssef, to identify a SHI transcription factor gene from maize which encodes the VRS2 transcription factor having at least 80% sequence identity to the amino acid of instant SEQ ID NO: 88, as taught by Youssef. Based on the teachings of Youssef, one of ordinary skill in the art would be motivated to mutate a maize VRS2 transcription factor gene knowing that the vrs2 mutants in barley produced premature stop codons. Thus, one of ordinary skill in the art would have a high expectation of success by following the teachings of Youssef.
The method of mutating an endogenous gene to disrupt DNA binding is a technique that was routine in the art at the time the application was filed, as taught by the cited reference and the state of the art in general.
In regard to claim 118, amino acid sequence A0A1I9RHG9_HORVU (UniProt) taught by Youssef, which shares 96.8% sequence identity with instant sequence SEQ ID NO: 88, is encoded by sequence KX601716.1 Hordeum vulgare mutant SHI (Vrs2) gene, vrs2.e allele, complete cds which shares 94% sequence identity with instant sequence SEQ ID NO: 75 (elected sequence; see alignment below) (i.e., wherein the target site comprises a sequence having at least 80% identity to the nucleotide sequence SEQ ID NO: 75).
Sequence ID: KX601716.1 aligned with instant sequence SEQ ID NO: 75
Query 15 CAGCTGCCAGGACTGCGGCAACCAGGCCAAGAAGGACTGCGTGCACCAGCGCTGCCGCAC 74
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Sbjct 1024 CAGCTGCCAGGACTGCGGCAACCAGGCCAAGAAGGACTGCCAGCACCAGCGCTGCCGCAC 1083
Query 75 CTGCTGCAAAAGCCGCGGCTTCGCCTGCAGCACCCACGTCAAGTCCACCTGGGT 128
|||||||||| ||| |||||||||||| ||||||||||||||||||||||||
Sbjct 1084 CTGCTGCAAATCCCGGGGCTTCGCCTGCTCCACCCACGTCAAGTCCACCTGGGT 1137
Response to Applicant’s Arguments
Applicant's arguments filed 05/20/2026 have been fully considered but they are not persuasive.
Applicant argues that Youssef fails to teach a guide nucleic acid that binds to a target site that encodes a sequence having at least 80% sequence identity to any one of SEQ ID NOs: 88-92.
The Examiner respectfully disagrees. The instant Specification states that the introduced mutation is intended to disrupt the binding of the encoded SHI family transcription factor to DNA (at least at page 2, line 5 and throughout the Specification). Therefore, it remains the position of this Office that any mutation introduced using any guide system in any gene location that disrupts the binding of DNA is rendered obvious by the teachings of Youssef. Youssef does not explicitly teach introducing a mutation using an editing system that comprises a guide nucleic acid; however, there is no way to distinguish a corn plant comprising a mutation introduced using an editing system that comprises a guide nucleic acid from a corn plant comprising a mutation introduced via X-ray, as taught by Youssef.
Youssef teaches that The SHI protein encoded by Vrs2 features two N-terminal zinc-finger-like motifs (CCCH) with a nuclear localiza-tion signal (KRRER) and the C-terminal SHI-family-specific IGGH domain (page 159, right column, first full paragraph).
INSTANT SEQ ID NO: 71 WITH (CCCH), (KRRER), AND IGGH DOMAINS HIGHLIGHTED
MAGFPLGGGS HTQSRDAPAS SVPPVHPSDA ASFLYAARAG AGLQLWQQQQ QHPFYTSNII
[AltContent: rect][AltContent: rect][AltContent: rect]RFSDDPPGPA PSLTGATSPS HRTRASGGSG GGGGVSCQDC GNQAKKDCVH QRCRTCCKSR
[AltContent: rect]GFACSTHVKS TWVSAAKRRE RQQQLAALAA SAGDTAAAAG PSRDPTKRPR ARLSVVTPTT
[AltContent: rect]TSSGDQQMVT VAERFPREVS SEALFRCVRL GPVDRAEAEV AYQTTVSIGG HVFKGLLHDV
GPRSLPAAGG GAAAAAIEYY FRHAADGSPP STTGAAGEAC GAGGVGNVVV SSAVVMDPYP
TPGSYAAFLP GAPFFPGGHP RQ
Youssef teaches sequence A0A1I9RHG9_HORVU which comprises the target region of instant sequence SEQ ID NO: 88 (two N-terminal zinc-finger-like motifs (CCCH)).
YOUSSEF SEQUENCE A0A1I9RHG9_HORVU WITH INSTANT SEQUENCE SEQ ID NO: 88 HIGHLIGHTED
[AltContent: rect]MAGFPLGTGGSGRDSPASPPGVHPSDASTFLYATRGGGFQLWGQPQDQHQHQHQLTHPFYASNLIRFATDDLPAGAAQSLAGAASSSSSRAARAAALAGGSAGTSCQDCGNQAKKDCQHQRCRTCCKSRGFACSTHVKSTWVPASKRRERQQQLTALAASAAATTAGAGPSRDPTSAPALDSPSPRRPPPRGISRW
Additionally, it is well known in the art that most zinc finger containing proteins (ZFPs) function as interaction modules that bind DNA, RNA, proteins, or other small, useful molecules (Gray, J., 2023, Grassius, https://grassius.org/family/Maize/C2H2, retrieved 07/30/2026). Given that there are only a finite number of targets in and around the N-terminal zinc-finger-like motifs (CCCH), it would have been obvious to a person of ordinary skill in the art to identify and test any one of these finite number of sequences and arrive at the guide nucleic acid as recited in the claims.
Applicant argues that Youssef does not teach a mutation within a target site having at least 80% sequence identity to any one of SEQ ID NOs: 88-92, and the disclosed mutants taught by Youssef all result in an early stop codon.
The Examiner respectfully disagrees. In addition to the teachings of Youssef in the above paragraphs, it is noted in Table 1 of the instant Specification (pages 93-94) that edited allele E is not in a region having at least 80% identity to nucleotide sequences SEQ ID NOs: 75, 76, or 83; additionally, edited alleles A, C, F, and H resulted in an early stop codon. Tables 2 and 3 (pages 96 and 97) display the results of 21 mutation combinations tested for ear height, kernel row number, and ear length. Of the listed 21 mutation combinations tested, only two mutation combinations (rows 6 and 17) did not include either allele A, C, E, F, or H. Thus, the mutations taught by Youssef align with several of the mutations taught in the instant invention.
Applicant argues that Youssef does not teach a mutant plant that has improved characteristics such as floret fertility, seed number, and/or seed weight.
Initially, it is noted that the claims do not require the Vrs2 mutated plants to display any improved characteristics. Turning again to Table 2, nine of the 21 mutation combinations had ear heights greater than the top of the range recorded for the control plants. However, the sample size for the majority of these mutation combinations was at most 2 plants, whereas the control group was 13 plants. As to the kernel row number, none of the mutation combinations were greater than the range of the control group. As for Table 3, only one mutation combination with a population of 1 sample plant fell slightly outside the top range for ear length. By relying on such small sample populations for testing, the results may easily be attributed to environmental factors.
When looking specifically at the sample plants that exclude either edited allele A, C, E, F, or H, Table 2 shows that the 13 control plants (WT, WT, WT) ranged from 91-114 for ear height and 14.3-18 for kernel row number. The 1 sample plant of Row 6 (heterozygous allele B, WT, homozygous allele G) showed an ear height of 118 and a kernel row number of 16; the 2 sample plants of Row 17 (WT, WT, homozygous allele G) showed ear heights of 94 and 106, and a kernel row numbers of 14 and 15.7. Similarly, In Table 3, the 13 control plants (WT, WT, WT) ranged from 13.4-16.55 for ear length. The 1 sample plant of Row 6 (heterozygous allele B, WT, homozygous allele G) showed an ear length of 12.55; the 2 sample plants of Row 17 (WT, WT, homozygous allele G) showed ear lengths of 12.85 and 15.15. Taken together, these results show that the plants comprising a mutation within the target site which do not result in an early stop codon did not perform better than the control plants in the parameters tested.
Youssef teaches the relationship between Vrs2, and barley inflorescence and shoot development. Youssef teaches that Vrs2 is specifically involved in floral organ patterning and phase duration by maintaining hormonal homeostasis and gradients during normal spike development and similarly influences plant stature traits (Youssef, Abstract, page 157). Youssef teaches the barley Vrs2, Vrs2 haplotype and vrs2 mutant allele (vrs2.e, int-b.3, int-b.6, int-b.75 and HOR19366) sequences (NCBI GenBank accession codes KX601696 to KX601720) (Youssef, Methods, Accession Codes, page 161). Youssef teaches that the protein encoded by Vrs2 features two N-terminal zinc-finger-like motifs (CCCH) with a nuclear localiza-tion signal (KRRER) and the C-terminal SHI-family-specific IGGH domain (page 159, right column, first full paragraph). Youssef teaches the classical row-type mutant six-rowed spike 2 (vrs2) deviates from this spike patterning insofar as it develops supernu-merary spikelets at its base and occasionally enlarged and fertile lateral spikelets toward the center of the spike (Youssef, page 157, right column, first paragraph). Thus, Youssef teaches all the components necessary to provide motivation for one of ordinary skill in the art to modify the VRS2 gene via a guide nucleic acid in maize.
Summary
No claim is 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.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTINA MEADOWS whose telephone number is (703)756-1430. The examiner can normally be reached Monday - Friday 9:00 am - 5:00 pm.
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/CHRISTINA L MEADOWS/Examiner, Art Unit 1663
CHRISTINA MEADOWS
Examiner
Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
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