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 .
Applicant’s response filed 01/09/2026 in reply to the office action of 10/14/2025 has been entered. Claims 1, 14, 28, 61, 69 and 72 are amended. Claim 3 is cancelled.
Claims 1, 4, 10-11, 14-16, 28, 34-35, 61, 65, 69, 71-72, 75, 80 and 100-102 are pending and examined.
Election/Restrictions
Applicant argues that withdrawn claim 14 depending from elected claim 1 and recites that the one or more nucleotide deletion or insertion is in a region having 80% sequence identity to SEQ ID NO: 75-108. Applicant also argues that SEQ ID NO: 75-108 are portions of the elected species of SEQ ID NO: 69-70 and SEQ ID NO: 72-73 as shown provided sequence alignments. Applicant’s arguments have been considered and are found to be persuasive. It is also noted that withdrawn claims 80 and 100-102 recite SEQ ID NO: 75-108. Therefore , claims 14, 80 and 100-102 is hereby rejoined with the elected invention.
Applicant further argues that claims 28 and 34-35 were not included in Group I or Group II . This is found persuasive because claims 28 and 34-35 are listed as group II. See paragraph bridging pages 2 and 3 of the office action of 10/14/2025. Claim 28 recites the non-elected invention of SEQ ID NO: 119, 121, 125 and 128 (CNRF6). Also, the sequences of SEQ ID NO: 101-108 are example portions or regions of CNR6 genomic sequences; and SEQ ID NO: 119, 121, 125 and 128 are example edited CNR6 genes, while SEQ ID NO: 120 and 122 are mutated CNR6 polypeptides encoded by SEQ ID NO: 119 and 121, respectively.
However, upon further search and consideration, the restriction requirement between Groups I and II and the species election have been withdrawn .
Withdrawn Objection and Rejection
The improper Markush rejection to the claims has been withdrawn in view of Applicant’s arguments that the CNR5 and CNR6 polynucleotides encode a cell number regulatory polypeptide that share the common structural feature of having a PLAC8 characterized by the presence of a cysteine-rich motive and at least one transmembrane domain. The 101 rejection and 112(a) rejection regarding written description have been withdrawn in view of Applicant’s amendment to the claims and/or upon further consideration.
Claim Rejections - 35 USC § 112
Claims 4, 65, 69 and 71- 72 remain rejected and 10-11, 14-15, 61, 75, 80 and 100-102 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. This rejection is repeated for the reasons of record as set forth in the last Office action. Applicant’s arguments have been considered but are not deemed persuasive.
As an initial matter, Applicant submits that claim 71 is included in rejection with no explanation, therefore, the rejection should be withdrawn. This is not found persuasive because claim 71 which depends from the rejected claim 61 does not obviate the rejection. Claim 71 limits the at least mutation to an “out-of-frame deletion” or “an out-of-frame insertion” that results in a premature stop codon. However, claim 61 (like claim 1) requires multiple mutations: parts (a) - (b) each recites 80% sequence identity to the full-length sequence of SEQ ID NO: 69, 70, 72 or 73, 80% sequence identity to the full length polypeptide sequence of SEQ ID NO: 71 or 74 , and a region having at least 80% identity to SEQ ID NO: 75-108; and wherein the target site is in a region having at least 80% sequence identity to anyone of SEQ ID NO: 75-108. It is unclear if the 80% sequence identity in target site is in addition to the 80% identity to the full-length sequences of parts (a) and (c). Furthermore, the multiple recitations of “and/or” in claim 61 renders the claims indefinite because it is not in the proper format of a Markush grouping, see MPEP 21 7305(h). A Markush group must be in the alternative and alternative expressions are permitted if they present no uncertainty or ambiguity with respect to the question of scope or clarity of the claims. Therefore, the metes and bounds of the mutations are unclear.
Applicant argues that the “at least one mutation” that is a base substitution, a base deletion, a base insertion and inversion” in claims 4 and 65 is not indefinite because Applicant asserts that 80% sequence identity in parent claims 1 and 61 is with reference to the sequence of the endogenous CNR gene and that “and/or” is defined on page 9, lines 7-8, of specification as “encompassing any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative ('or')." Applicant refers to Table 2 of the specification which shows that Allele 2 has a single type of mutation (a deletion), whereas Allele 1 has two different types of mutations (a deletion and an inversion). Applicant, therefore, requests withdrawal of the rejection.
These arguments are not found persuasive for the following reasons: 1) each of claim 1 and claim 61 requires multiple of mutations: parts (a) and (b) each recites 80% sequence identity to the full-length sequence of SEQ ID NO: 69, 70, 72 or 73; 80% sequence identity to the full length encoded polypeptide sequence of SEQ ID NO: 71 or 74 ; and a region having at least 80% identity to SEQ ID NO: 75-108; and wherein the target site is in a region having at least 80% sequence identity to anyone of SEQ ID NO: 75-108. It is unclear if the 80% sequence identity in target site is in addition to the 80% identity to the full-length sequences of parts (a) - (c). 2) The multiple recitation of “and/or” in claim 61 renders the claims indefinite because it is not in the proper format of a Markush grouping. See MPEP 21 7305(h). A Markush group must be in the alternative and alternative expressions are permitted if they present no uncertainty or ambiguity with respect to the question of scope or clarity of the claims. 3) Although a claim should be interpreted in light of the specification disclosure, it is generally considered improper to read limitations contained in the specification into the claims. See In re Prater, 415 F.2d 1393, 162 USPQ 541 (CCPA 1969) and In re Winkhaus, 527 F.2d 637, 188 USPQ 129 (CCPA 1975), which discuss the premise that one cannot rely on the specification to impart limitations to the claim that are not recited in the claim. The limitations on Table 2 of the specification which shows that Allele 2 has a single type of mutation (a deletion), and Allele 1 has two different types of mutations (a deletion and an inversion) are not recited in the rejected claims.
Applicant asserts that the amendment to claim 69 to delete the optional part would obviate the rejection. However, claim 69 depends from the rejected claim 61 which requires multiple of mutations: parts (a) and (b) each recites 80% sequence identity to the full-length sequence of SEQ ID NO: 69, 70, 72 or 73, 80% sequence identity to the full length polypeptide sequence of SEQ ID NO: 71 or 74 , and a region having at least 80% identity to SEQ ID NO: 75-108; and where in the target site is in a region having at least 80% sequence identity to anyone of SEQ ID NO: 75-108. It is unclear if the 80% sequence identity in target site is in addition to the 80% identity to the full-length sequences of parts (a)-(c).
The rejection also applies to claims dependent claims 10-11, 14 and 71-72 because one cannot determine the specific location where the “out-of-frame insertion” or “out-of- frame deletion” or “inversion” mutation is present, given that the mutations in parent claims 1 and 61 is indefinite. Dependent claims, that don’t obviate the rejection, are included in the rejection.
Claim 80 is rejected as being indefinite because SEQ ID NO: 75-100, 102-104 and/or 106-108, are not spacer sequences. According to page 7 of the specification, SEQ ID NO: 109-114 are the spacer sequences. Correction and/or clarification is required to more clearly define the metes and bounds of the claims.
Therefore, for all the reasons discussed above the rejection is proper and maintained.
Claim Rejections - 35 USC § 102
Claims 1, 4, 14-15, and 102 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Guo et al (WO 2006/012024; Applicant’s IDS) or Guo Mei et al (The Plant Cell (2010) vol.22 (4):1057-1073; Applicant’s IDS). This rejection is repeated for the reasons of record as set forth in the last Office action. Applicant’s arguments have been considered but are not deemed persuasive.
Applicant asserts that the amendment to claim 1 to recite the at least one mutation is in a region having at least 80% sequence identity to any of SEQ ID NO: 75-108, would obviate the rejection. Applicant argues that the nucleotide sequence Guo (2006) differs two nucleotides from Applicant’s nucleotide sequence of SEQ ID NO: 71 and the mutation does not locate in any of the region of SEQ ID NO: 75-108. Applicant also argues that Guo (2010) teaches a nucleotide sequence that is 100% identical to the claimed sequences and does not comprise at least one mutation. Applicant further argues that the full polypeptide sequence of the prior art is less than 90% identical to Applicant’s SEQ ID NO: 116, 118, 120, 122, 124, 127 or 130. Applicant’s, therefore, request withdrawal of the rejection.
These arguments have been considered but are not deemed persuasive because of the following reasons: 1) The amendment to claim 1 to recite “at least one mutation is in a region having at least 80% sequence identity to any one of SEQ ID NO: 75-108” together with the “80% sequence identity” to multiple full length nucleotide (SEQ ID NO: 69-70 or 73) and 80% sequence identity to encoded polypeptide sequences of SEQ OD NO: 72 and 74 does not distinguish from the prior art sequence. See the 112(b) rejection above. 2) Guo et al teach the CNR5 and CNR6 (Cell Number Regulator) genes known to be involved in controlling cell number, fruit size, ear length and yield-related parameters, and teach that the downregulation of gene expression by mutation (claims 1-24; pages 1-10, 71, 84-85 and Figs 1-2) improves yield. 3) The “at least one mutation in a region having at least 80% or 90% sequence identity to any of SEQ ID NO: 75-108 reads on a sequence with 5 nucleotides (as defined on page 24 of the specification) in SEQ ID NO: 9-12 of the prior art. Therefore, the “at least one mutation” required by the claims is not specific. 4) With regard to Applicant’s arguments that Guo (2010) sequence is 100% to Applicant’s SEQ ID NO: 70, it is noted that the “at least 80%” recited in the claims includes 100% sequence identity (see definition of “at least 80%” on page 51, lines 10-12), and the non-specific “at least one mutation” encompasses naturally occurring allelic variants/polymorphism of CNR genes in maize genome. Table 1 of Guo (2010) shows correlation between downregulation of the CNR genes and increased maize plant growth and ear size. 5) each of Guo (2006) and Guo (2010) teaches a method of decreasing the CNR polypeptide by introducing an antisense nucleotide sequence of SEQ ID NO: 9 or 11 into a plant cell, wherein the nucleotide sequence inhibits expression of the endogenous CNR polypeptide, and the plant exhibits increased seed size and enhanced root growth as a result of the decreased CNR polypeptide activity in the plant (claims 13-24 of Guo 2006). 6) Regarding the full polypeptide sequence having at least 90% identical to Applicant’s SEQ ID NO: 116, 118, 120, 122, 124, 127 or 130; it is noted that claims 16 and 75 are not included in this rejection. Therefore, for all the reasons discussed above and because of the 112(b) rejection above, the rejection is proper and maintained.
SEQ ID NO: 70 or a DNA encoding SEQ ID NO: 71
RESULT 3
AEF69699
ID AEF69699 standard; DNA; 1009 BP.
XX
AC AEF69699;
XX
DT 06-APR-2006 (first entry)
XX
DE DNA encoding maize cell number regulator, ZmCNR 5.
XX
KW transgenic plant; seed; crop improvement; ds; gene.
XX
OS Zea mays.
XX
FH Key Location/Qualifiers
FT CDS 148..702
FT /*tag= a
FT /product= "ZmCNR 5"
XX
CC PN WO2006012024-A2.
XX
CC PD 02-FEB-2006.
XX
CC PF 16-JUN-2005; 2005WO-US021232.
XX
PR 28-JUN-2004; 2004US-0583340P.
XX
CC PA (PION-) PIONEER HI-BRED INT INC.
XX
CC PI Guo M, Simmons CR, Hershey HP;
XX
DR WPI; 2006-125907/13.
DR P-PSDB; AEF69700.
XX
CC PT New isolated cell number regulator (CNR) polynucleotides and
CC PT polypeptides, useful for producing transgenic plants and seeds having
CC PT improved phenotypes, e.g. enhanced root growth, increased seed size, or
CC PT increased seed weight.
XX
CC PS Claim 1; SEQ ID NO 9; 120pp; English.
XX
CC The invention relates to an isolated polynucleotide. The polynucleotides
CC and polypeptides are useful for producing transgenic plants and seeds
CC having improved phenotypes, e.g. enhanced root growth, increased seed
CC size, increased seed weight, increased embryo size, increased leaf size,
CC increased seedling vigor, enhanced silk emergence, or increased ear size.
CC It can also be used for producing heterotic plants, which are more robust
CC and of larger stature. The present sequence represents the DNA encoding a
CC maize cell number regulator.
XX
SQ Sequence 1009 BP; 260 A; 204 C; 256 G; 289 T; 0 U; 0 Other;
Length: 1009
Score: 1022.00 Matches: 183
Percent Similarity: 99.5% Conservative: 0
Best Local Similarity: 99.5% Mismatches: 1
Query Match: 99.5% Indels: 0
Gaps: 0
US-18-364-482-71 (1-184) x AEF69699 (1-1009)
Qy 1 MetAlaGlyLysGlySerTyrValProProGlnTyrIleProLeuTyrSerLeuAspThr 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 148 ATGG]CTGGAAAAGGAAGCTATGTACCTCCACAATATATTCCCTTATACAGCCTAGATACC 207
Qy 21 GluGluAspArgValProAlaValGluGluAsnHisAlaThrArgProLysLeuAsnGln 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 208 GAAGAGGATCGTGTCCCTGCCGTGGAAGAGAACCATGCTACGCGCCCTAAACTAAACCAG 267
Qy 41 AspProThrGlnTrpSerSerGlyIleCysAlaCysPheAspAspProGlnSerCysCys 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 268 GATCCAACACAATGGTCATCTGGCATCTGTGCCTGTTTTGATGACCCCCAGAGCTGTTGT 327
Qy 61 IleGlyAlaIleCysProCysPheLeuPheGlyLysAsnAlaGlnPheLeuGlySerGly 80
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Db 328 ATTGGTGCGACTTGCCCCTGTTTCCTTTTTGGAAAGAATGCACAATTCTTGGGATCTGGA 387
Qy 81 ThrLeuAlaGlySerCysThrThrHisCysMetLeuTrpGlyLeuLeuThrSerLeuCys 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 388 ACTCTTGCTGGATCATGCACTACACATTGCATGTTGTGGGGCCTTCTCACAAGTCTATGC 447
Qy 101 CysValPheThrGlyGlyLeuValLeuAlaValProGlySerAlaValAlaCysTyrAla 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 448 TGTGTATTTACTGGAGGTCTAGTATTAGCAGTTCCAGGATCTGCCGTTGCTTGTTATGCT 507
Qy 121 CysGlyTyrArgSerAlaLeuArgThrLysTyrAsnLeuProGluAlaProCysGlyAsp 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 508 TGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGGAAGCACCCTGTGGCGAT 567
Qy 141 LeuThrThrHisLeuPheCysHisLeuCysAlaIleCysGlnGluTyrArgGluIleArg 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 568 TTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGT 627
Qy 161 GluArgThrGlySerGlySerSerProAlaProAsnValThrProProProValGlnThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 628 GAGAGAACAGGCAGTGGCTCCTCACCAGCTCCTAATGTGACTCCACCTCCAGTTCAGACG 687
Qy 181 MetAspGluLeu 184
||||||||||||
Db 688 ATGGATGAGCTT 699
SEQ ID NO: 70
RESULT 3
AEF69699
ID AEF69699 standard; DNA; 1009 BP.
XX
AC AEF69699;
XX
DT 06-APR-2006 (first entry)
XX
DE DNA encoding maize cell number regulator, ZmCNR 5.
XX
KW transgenic plant; seed; crop improvement; ds; gene.
XX
OS Zea mays.
XX
FH Key Location/Qualifiers
FT CDS 148..702
FT /*tag= a
FT /product= "ZmCNR 5"
XX
CC PN WO2006012024-A2.
XX
CC PD 02-FEB-2006.
XX
CC PF 16-JUN-2005; 2005WO-US021232.
XX
PR 28-JUN-2004; 2004US-0583340P.
XX
CC PA (PION-) PIONEER HI-BRED INT INC.
XX
CC PI Guo M, Simmons CR, Hershey HP;
XX
DR WPI; 2006-125907/13.
DR P-PSDB; AEF69700.
XX
CC PT New isolated cell number regulator (CNR) polynucleotides and
CC PT polypeptides, useful for producing transgenic plants and seeds having
CC PT improved phenotypes, e.g. enhanced root growth, increased seed size, or
CC PT increased seed weight.
XX
CC PS Claim 1; SEQ ID NO 9; 120pp; English.
XX
CC The invention relates to an isolated polynucleotide. The polynucleotides
CC and polypeptides are useful for producing transgenic plants and seeds
CC having improved phenotypes, e.g. enhanced root growth, increased seed
CC size, increased seed weight, increased embryo size, increased leaf size,
CC increased seedling vigor, enhanced silk emergence, or increased ear size.
CC It can also be used for producing heterotic plants, which are more robust
CC and of larger stature. The present sequence represents the DNA encoding a
CC maize cell number regulator.
XX
SQ Sequence 1009 BP; 260 A; 204 C; 256 G; 289 T; 0 U; 0 Other;
Query Match 99.4%; Score 551.8; Length 1009;
Best Local Similarity 99.6%;
Matches 553; Conservative 0; Mismatches 2; Indels 0; Gaps 0;
Qy 1 ATGGCTGGAAAAGGAAGCTATGTACCTCCACAATATATTCCCTTATACAGCCTAGATACC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 148 ATGGCTGGAAAAGGAAGCTATGTACCTCCACAATATATTCCCTTATACAGCCTAGATACC 207
Qy 61 GAAGAGGATCGTGTCCCTGCCGTGGAAGAGAACCATGCTACGCGCCCTAAACTAAACCAG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 208 GAAGAGGATCGTGTCCCTGCCGTGGAAGAGAACCATGCTACGCGCCCTAAACTAAACCAG 267
Qy 121 GATCCAACACAATGGTCATCTGGCATCTGTGCCTGTTTTGATGACCCCCAGAGCTGTTGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 268 GATCCAACACAATGGTCATCTGGCATCTGTGCCTGTTTTGATGACCCCCAGAGCTGTTGT 327
Qy 181 ATTGGTGCGATTTGCCCCTGTTTCCTTTTTGGAAAGAATGCACAATTCTTGGGATCTGGA 240
|||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||
Db 328 ATTGGTGCGACTTGCCCCTGTTTCCTTTTTGGAAAGAATGCACAATTCTTGGGATCTGGA 387
Qy 241 ACTCTTGCTGGATCATGCACTACGCATTGCATGTTGTGGGGCCTTCTCACAAGTCTATGC 300
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 388 ACTCTTGCTGGATCATGCACTACACATTGCATGTTGTGGGGCCTTCTCACAAGTCTATGC 447
Qy 301 TGTGTATTTACTGGAGGTCTAGTATTAGCAGTTCCAGGATCTGCCGTTGCTTGTTATGCT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 448 TGTGTATTTACTGGAGGTCTAGTATTAGCAGTTCCAGGATCTGCCGTTGCTTGTTATGCT 507
Qy 361 TGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGGAAGCACCCTGTGGCGAT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 508 TGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGGAAGCACCCTGTGGCGAT 567
Qy 421 TTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGT 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 568 TTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGT 627
Qy 481 GAGAGAACAGGCAGTGGCTCCTCACCAGCTCCTAATGTGACTCCACCTCCAGTTCAGACG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 628 GAGAGAACAGGCAGTGGCTCCTCACCAGCTCCTAATGTGACTCCACCTCCAGTTCAGACG 687
Qy 541 ATGGATGAGCTTTGA 555
|||||||||||||||
Db 688 ATGGATGAGCTTTGA 702
SEQ ID NO: 70
RESULT 3
AEF69699
ID AEF69699 standard; DNA; 1009 BP.
XX
AC AEF69699;
XX
DT 06-APR-2006 (first entry)
XX
DE DNA encoding maize cell number regulator, ZmCNR 5.
XX
KW transgenic plant; seed; crop improvement; ds; gene.
XX
OS Zea mays.
XX
FH Key Location/Qualifiers
FT CDS 148..702
FT /*tag= a
FT /product= "ZmCNR 5"
XX
CC PN WO2006012024-A2.
XX
CC PD 02-FEB-2006.
XX
CC PF 16-JUN-2005; 2005WO-US021232.
XX
PR 28-JUN-2004; 2004US-0583340P.
XX
CC PA (PION-) PIONEER HI-BRED INT INC.
XX
CC PI Guo M, Simmons CR, Hershey HP;
XX
DR WPI; 2006-125907/13.
DR P-PSDB; AEF69700.
XX
CC PT New isolated cell number regulator (CNR) polynucleotides and
CC PT polypeptides, useful for producing transgenic plants and seeds having
CC PT improved phenotypes, e.g. enhanced root growth, increased seed size, or
CC PT increased seed weight.
XX
CC PS Claim 1; SEQ ID NO 9; 120pp; English.
XX
CC The invention relates to an isolated polynucleotide. The polynucleotides
CC and polypeptides are useful for producing transgenic plants and seeds
CC having improved phenotypes, e.g. enhanced root growth, increased seed
CC size, increased seed weight, increased embryo size, increased leaf size,
CC increased seedling vigor, enhanced silk emergence, or increased ear size.
CC It can also be used for producing heterotic plants, which are more robust
CC and of larger stature. The present sequence represents the DNA encoding a
CC maize cell number regulator.
XX
SQ Sequence 1009 BP; 260 A; 204 C; 256 G; 289 T; 0 U; 0 Other;
Length: 1009
Score: 1022.00 Matches: 183
Percent Similarity: 99.5% Conservative: 0
Best Local Similarity: 99.5% Mismatches: 1
Query Match: 99.5% Indels: 0
Gaps: 0
US-18-364-482-71 (1-184) x AEF69699 (1-1009)
Qy 1 MetAlaGlyLysGlySerTyrValProProGlnTyrIleProLeuTyrSerLeuAspThr 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 148 ATGGCTGGAAAAGGAAGCTATGTACCTCCACAATATATTCCCTTATACAGCCTAGATACC 207
Qy 21 GluGluAspArgValProAlaValGluGluAsnHisAlaThrArgProLysLeuAsnGln 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 208 GAAGAGGATCGTGTCCCTGCCGTGGAAGAGAACCATGCTACGCGCCCTAAACTAAACCAG 267
Qy 41 AspProThrGlnTrpSerSerGlyIleCysAlaCysPheAspAspProGlnSerCysCys 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 268 GATCCAACACAATGGTCATCTGGCATCTGTGCCTGTTTTGATGACCCCCAGAGCTGTTGT 327
Qy 61 IleGlyAlaIleCysProCysPheLeuPheGlyLysAsnAlaGlnPheLeuGlySerGly 80
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Db 328 ATTGGTGCGACTTGCCCCTGTTTCCTTTTTGGAAAGAATGCACAATTCTTGGGATCTGGA 387
Qy 81 ThrLeuAlaGlySerCysThrThrHisCysMetLeuTrpGlyLeuLeuThrSerLeuCys 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 388 ACTCTTGCTGGATCATGCACTACACATTGCATGTTGTGGGGCCTTCTCACAAGTCTATGC 447
Qy 101 CysValPheThrGlyGlyLeuValLeuAlaValProGlySerAlaValAlaCysTyrAla 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 448 TGTGTATTTACTGGAGGTCTAGTATTAGCAGTTCCAGGATCTGCCGTTGCTTGTTATGCT 507
Qy 121 CysGlyTyrArgSerAlaLeuArgThrLysTyrAsnLeuProGluAlaProCysGlyAsp 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 508 TGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGGAAGCACCCTGTGGCGAT 567
Qy 141 LeuThrThrHisLeuPheCysHisLeuCysAlaIleCysGlnGluTyrArgGluIleArg 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 568 TTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGT 627
Qy 161 GluArgThrGlySerGlySerSerProAlaProAsnValThrProProProValGlnThr 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 628 GAGAGAACAGGCAGTGGCTCCTCACCAGCTCCTAATGTGACTCCACCTCCAGTTCAGACG 687
Qy 181 MetAspGluLeu 184
||||||||||||
Db 688 ATGGATGAGCTT 699
Claim Rejections - 35 USC § 103
Claims 1, 4, 10-11, 14-16, 28, 34-35, 61, 65, 69, 71-72, and 75 remain rejected, claims 80 and 100-102 are rejected under 35 U.S.C. 103 as being unpatentable over each of Guo et al (WO 2006/012024; Applicant’s IDS) and Guo Mei et al (The Plant Cell (2010) vol.22 (4):1057-1073) in view of Jiang et al (ACS Agri. Sci Technol (2022)2:174-183; Applicant’s IDS) and Xu et al (Planta(2013) 238: 643-655; Applicant’s IDS). This rejection is repeated for the reasons of record as set forth in the last Office action. Applicant’s arguments have been considered but are not deemed persuasive.
Applicant argues that Guo 2006 and Guo (2010) fail to teach or suggest the amended reciting "the at least one mutation is in a region having at least 80% sequence identity to any of SEQ ID NOs:75-108” in claim 1 , and "the target site in the endogenous CNR gene is in a region having at least 80% sequence identity to any of SEQ ID NOs:75-108”, in claim 61. Applicant also argues that Jiang, cited for describing a method of using the CRISPR-Cas editing system to modify endogenous genes in the maize genome, fails to describe editing of a CNR gene by targeting a region having at least 80% sequence identity to any of SEQ ID NOs:75-108. Applicant further argues that Xu describes the molecular characterization of rice FW2.2 genes and two T-DNA mutant lines. Therefore, each of Jiang and Xu fails to compensate for the deficiencies in Guo 2006 and Guo 2010, and also fails to provide any reasonable expectation of success to arrive the claimed invention. Applicant requests withdrawal of the rejection.
These arguments have been fully considered but are not deemed persuasive because of the following reasons: 1) Guo (2006) is relied upon because it provides not only the nucleotide and polypeptide sequences of the maize CNR5 and CNR6 (Cell Number Regulator) genes but also provides that the downregulation of CNR genes expression by mutation improves yield-related traits including increased fruit number or size, and improved ear length. The CNR5 and CNR6 genes of the prior art share 100% and 99.59% sequence identity to Applicant’s SEQ ID NO: 70 and 73, respectively (see the alignment of sequences shown below). At pages 46-55, Guo et al teach various methods of inhibiting the expression of the CNR genes in a plant including sense or antisense suppression targeting all or part of the 5’ or 3’ untranslated region of the CNR gene, or by targeting all or part of the coding sequences , or by double stranded RNA interference, gene disruption by inserting a transposon within the 5’ or 3’untranslated region or the coding region of the gene encoding CNR polypeptide, insertional mutations in gene exons that result in null mutants. At page 55, Guo (2006) describes methods for decreasing or eliminating the expression of endogenous CNR genes in plants including deletion mutagenesis. Mutations in conserved residues to generate variants of the CNR sequences are also described in Example 9 on pages 84-87. 2) Guo (2010) is cited in Xu et al (2013) that teach CNR1 as a homolog of the Fruit-Weight2.2-like gene of tomato and which is also a negative plant/cell regulator. Xu et al describe the FW2.2 and its plant homologs as having proteins with a highly conserved core motif (one or two transmembrane motifs locating between two cysteine/proline-rich domains. Xu et al also describe two mutants (osfwl3 and osfwl5), one with increased grain weight and the other with increased plant height by 5.3 and 12.5%, respectively, as compared to wild type as well the method of producing said mutants. 3) Jiang et al is relied upon because it provide Crispr-Cas editing system to modify endogenous genes in maize genome to improve desired traits including yield and yield related traits (Table 1 on pages 175 to 176) which also has been applied to other crops including rice, wheat, tomato, and potato. At page 176, Jiang et al teach using the Crispr-Cas system to knock out alleles of a yield-related gene in maize that resulted in increased grain yield and kernel numbers as compared to wild type plants. Fig. 1 on page 177 shows the Crispr-Cas technology and its application in maize improvement. 4) Applicant’s arguments on pages 12-13 to overcome the written description rejection supports the 103 art rejection. Applicant’s arguments are as follows:
“……the claimed CNR gene encodes a CNR polypeptide, which is described in the specification and art as including a PLAC8 domain characterized by the presence of a cysteine-rich CXXXXXCPC motif and at least one transmembrane domain that is responsible for membrane transport activity……….. The as filed specification also describes nucleotide sequences having 80% sequence identity to CNR gene as
including, e.g., homologs, that may be identified by methods such as computer-based alignments and hybridization under stringent conditions. ………Indeed, at the time of filing of the specification, one of ordinary skill in the art would have appreciated that two nucleotide sequences sharing 80% sequence identity may still encode the same protein. Accordingly, not only does the specification describe sequences having at least 80% sequence identity to those recited in the claims, the specification provides specific guidance for identifying such sequences by both structure and function”.
5) With regard to Applicant’s argument that the prior art does not teach or suggest a sequence having at least 90% identity to anyone of SEQ ID NOs:115, 117, 123, 126, 129 or encodes a mutated CRN polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:116, 118, 124, 127 or 130, it is noted that the part that recites a sequence having at least 90% identity to anyone of SEQ ID NOs:115, 117, 123, 126, 129 or encodes a mutated CRN polypeptide having at least 90% sequence identity to any one of SEQ ID NOs:116, 118, 124, 127 or 130 in claims 100-101, is “optional”.
With regard to claim 80 (and 28, 34-35), drawn to a guide nucleic acid that binds to a target site in a CNR gene, wherein the target site is within a region of the CNR gene having at least 80% identity to any of SEQ ID NO: 75-108; it is noted that Guo et al (2010) teach a genomic region that is 100% identical to Applicant’s SEQ ID NO:95, and a plant/cell comprising said mutated CNR gene. See the alignment of sequences between Applicant’s SEQ ID NO: 95 and SEQ ID NO: 9 of Guo et al (2010):
Search Results from Applicant’s SEQ ID NO: 95
RESULT 2
HM008657
LOCUS HM008657 555 bp mRNA linear PLN 12-JUN-2010
DEFINITION Zea mays cell number regulator 5 (CNR05) mRNA, complete cds.
ACCESSION HM008657
ORGANISM Zea mays
REFERENCE 1 (bases 1 to 555)
AUTHORS Guo,M.,
TITLE Cell Number Regulator1 affects plant and organ size in maize:
implications for crop yield enhancement and heterosis
JOURNAL Plant Cell 22 (4), 1057-1073 (2010)
PUBMED 20400678
REFERENCE 2 (bases 1 to 555)
AUTHORS Guo,M., Rupe,M.A., Dieter,J.A., Zou,J., Spielbauer,D., Duncan,K.E.,
Howard,R.J., Hou,Z. and Simmons,C.R.
TITLE Direct Submission
JOURNAL Submitted (16-MAR-2010) Agronomic Traits, Pioneer Hi-Bred
International, Inc., 7250 NW 62nd Ave., Johnston, IA 50131, USA
FEATURES Location/Qualifiers
source 1..555
/organism="Zea mays"
/mol_type="mRNA"
/cultivar="B73"
/db_xref="taxon:4577"
gene 1..555
/gene="CNR05"
/note="ZmCNR05"
CDS 1..555
/gene="CNR05"
/codon_start=1
/product="cell number regulator 5"
/protein_id="ADI48419.1"
/translation="MAGKGSYVPPQYIPLYSLDTEEDRVPAVEENHATRPKLNQDPTQ
WSSGICACFDDPQSCCIGAICPCFLFGKNAQFLGSGTLAGSCTTHCMLWGLLTSLCCV
FTGGLVLAVPGSAVACYACGYRSALRTKYNLPEAPCGDLTTHLFCHLCAICQEYREIR
ERTGSGSSPAPNVTPPPVQTMDEL"
ORIGIN
Query Match 100.0%; Score 104; Length 555;
Best Local Similarity 100.0%;
Matches 104; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 406 GCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAG 465
Qy 61 TACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCTCACCAGC 104
||||||||||||||||||||||||||||||||||||||||||||
Db 466 TACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCTCACCAGC 509
Claims 16 and 75 are included in the 103 rejection because Guo (2006) teach a mutated CNR6 polypeptide having at least 92% sequence identity to Applicant’s SEQ ID NO: 120. See the alignment of sequences shown below:
Search Results of instant SEQ ID NO: 120
RESULT 2
AEF69701
ID AEF69701 standard; DNA; 976 BP.
XX
AC AEF69701;
XX
DT 06-APR-2006 (first entry)
XX
DE DNA encoding maize cell number regulator, ZmCNR 6.
XX
KW transgenic plant; seed; crop improvement; ds; gene.
XX
OS Zea mays.
XX
FH Key Location/Qualifiers
FT CDS 66..785
FT /*tag= a
FT /product= "ZmCNR 6"
XX
CC PN WO2006012024-A2.
XX
CC PD 02-FEB-2006.
XX
CC PF 16-JUN-2005; 2005WO-US021232.
XX
PR 28-JUN-2004; 2004US-0583340P.
XX
CC PA (PION-) PIONEER HI-BRED INT INC.
XX
CC PI Guo M, Simmons CR, Hershey HP;
XX
DR WPI; 2006-125907/13.
DR P-PSDB; AEF69702.
XX
CC PT New isolated cell number regulator (CNR) polynucleotides and
CC PT polypeptides, useful for producing transgenic plants and seeds having
CC PT improved phenotypes, e.g. enhanced root growth, increased seed size, or
CC PT increased seed weight.
XX
CC PS Claim 1; SEQ ID NO 11; 120pp; English.
XX
CC The invention relates to an isolated polynucleotide. The polynucleotides
CC and polypeptides are useful for producing transgenic plants and seeds
CC having improved phenotypes, e.g. enhanced root growth, increased seed
CC size, increased seed weight, increased embryo size, increased leaf size,
CC increased seedling vigor, enhanced silk emergence, or increased ear size.
CC It can also be used for producing heterotic plants, which are more robust
CC and of larger stature. The present sequence represents the DNA encoding a
CC maize cell number regulator.
XX
SQ Sequence 976 BP; 232 A; 254 C; 288 G; 202 T; 0 U; 0 Other;
Length: 976
Score: 1210.00 Matches: 221
Percent Similarity: 92.5% Conservative: 0
Best Local Similarity: 92.5% Mismatches: 0
Query Match: 97.7% Indels: 18
Gaps: 2
US-18-364-482-120 (1-221) x AEF69701 (1-976)
Qy 1 MetAlaGluAspAlaThrSerSerHisProSerArgTyrValLysLeuThrLysAspGln 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 66 ATGGCGGAGGATGCTACGAGCAGCCACCCGTCACGCTACGTCAAGCTCACCAAGGACCAG 125
Qy 21 AspAlaProAlaGluAspIleArgProGlyGluLeuAsnGlnProValHisValProGln 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 126 GACGCCCCCGCCGAGGACATCCGCCCCGGCGAGCTCAACCAGCCAGTTCACGTCCCGCAG 185
Qy 41 LeuGluGlyArgArgCysSerGluCysGlyGlnValLeuProGluSerTyrGluProPro 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 186 CTCGAAGGCCGGAGGTGTAGCGAGTGCGGTCAGGTCCTGCCCGAGAGCTACGAGCCGCCC 245
Qy 61 AlaAspGluProTrpThrThrGlyIlePheGlyCysThrAspAspProGluThrCysArg 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 246 GCCGACGAGCCCTGGACCACCGGGATCTTCGGATGCACCGATGACCCAGAGACCTGCCGA 305
Qy 81 ThrGlyLeuPheCysProCysValLeuPheGlyArgAsnValGluAlaValArgGluAsp 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 306 ACTGGATTGTTTTGCCCCTGCGTGCTGTTTGGGCGCAACGTTGAGGCTGTTAGGGAGGAC 365
Qy 101 IleProTrpThrThrProCysValCysHisAlaValPheValGluGlyGlyIleThrLeu 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 366 ATCCCTTGGACAACTCCTTGCGTGTGCCATGCTGTATTCGTTGAAGGAGGGATCACGCTG 425
Qy 121 AlaIle------------------------------------------LeuIleGlyGlu 126
|||||| ||||||||||||
Db 426 GCGATTCTGACGGCGATATTTCACGGTGTTGATCCGAGGACGTCATTCCTGATTGGAGAA 485
Qy 127 GlyLeuValPheSerTrpTrpLeuCysAlaThrTyrThrGlyIlePheArgGlnGlyLeu 146
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 486 GGTCTGGTGTTCAGCTGGTGGTTATGTGCTACCTACACTGGCATCTTCCGCCAGGGGCTT 545
Qy 147 ------------HisLeuLysAsnSerProCysAspProCysMetValHisCysCysLeu 162
||||||||||||||||||||||||||||||||||||||||||||||||
Db 546 CAGAGGAAATATCATCTCAAGAACTCTCCGTGTGACCCATGCATGGTCCACTGCTGCTTG 605
Qy 163 HisTrpCysAlaAsnCysGlnGluHisArgGluArgThrGlyArgLeuAlaGluAsnAsn 182
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 606 CACTGGTGTGCCAACTGCCAGGAGCATCGCGAGAGGACGGGACGGCTTGCAGAGAACAAC 665
Qy 183 AlaValProMetThrValValAsnProProProValGlnGluMetSerMetLeuGluGlu 202
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 666 GCAGTGCCCATGACGGTTGTGAACCCGCCTCCGGTGCAAGAGATGAGCATGCTGGAGGAG 725
Qy 203 ValGluGluLysGlyAlaGluLysSerGluHisAspAspValGluValIleProLeu 221
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 726 GTGGAGGAGAAGGGAGCAGAGAAGAGTGAACACGATGATGTGGAGGTCATTCCTCTA 782
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use one or more of the gene expression inhibiting techniques of reducing CNR gene expression in plants to produce modified plants or plant parts exhibiting increased yield and yield related traits as taught by each of Guo et al and Guo Mei et al, and to modify that method by incorporating the Crispr-Cas system taught by Jiang et al to modify specific sites in endogenous known CNR genes and generate mutants or mutant alleles in any plant species with a reasonable expectation of success as taught by each of Guo et al and Jiang et al. One would have been motivated to use Crispr-Cas based genome editing as an alternative to the other gene expression inhibiting technology, given its simple operation, low cost and high efficiency that has been successfully applied to many crops in the development of non-genetically modified (Non-GMO) crops with the desired traits as taught by Jiang et al.
Therefore, for all the reasons discussed above, the claimed invention is a prima facie obvious as evidenced by the references, especially in the absence of evidence to the contrary.
Pertinent Prior Art:
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Zhang et al (Journal of Advanced Research(2021) 29:207-221) teach Crispr-Cas as a power tool for gene modification and for improving crop yield.
Li et al (Frontiers in Plant Science (2022)13:1-11) teach Crispr-Cas mediated genome editing to accelerate yield enhancement.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MEDINA AHMED IBRAHIM whose telephone number is (571)272-0797. The examiner can normally be reached Monday-Friday, 9:00 - 6:00.
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MEDINA AHMED. IBRAHIM
Primary Examiner
Art Unit 1662
/MEDINA A IBRAHIM/Primary Examiner, Art Unit 1662
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