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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/03/2025 has been entered.
Claims 1, 7, 8, 12, 15, 22, 24, 30, 34, 50, 56-57, 60-62 and 84-86 are pending and examined.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 7, 8, 15, 22, 24, 30 and 34 are rejected under 35 U.S.C. 102(a)(1) as being clearly anticipated by Gao, X. et al., MPMI (2007) Vol. 20, No. 8; pp. 922-933 in light of Gao (2008) Molecular Plant-Microbe Interactions, 21 (1): 98-109 and in light of Wilson (2001) Molecular Plant-Microbe Interactions; Vol. 14, no. 8; pp.980-987.
The claims are broadly drawn to a maize plant, or part thereof; or maize plant cell having a mutation in at least one endogenous LOX gene encoding a LOX protein; wherein the mutation is in a LOX gene
having at least 90% identity to a LOX polynucleotide sequence of SEQ ID NO: 72, 75, 78, or 81; or 90% thereof; or
that encodes a polypeptide having the amino acid sequence of SEQ ID NO: 74, 77, 80, or 83; or 95% thereof; or
comprises the LOX polynucleotide of 73, 76, 79, or 82 or 90% thereof; or
wherein the mutated LOX gene comprises a nucleotide sequence of SEQ ID NO: 94, 96, 97-105, or 106; or
wherein the mutation is within a target site of said LOX gene as recited in claim 24; and
wherein the plant acquires resistance to ear rot and/or stalk rot compared to a maize plant without the mutation.
Gao (2007) teaches a knockout of maize LOX3 by a Mu (mutator) transposon insertion into exon 5 of the endogenous Maize LOX3 gene allele lox3-4 on page 923 (see lox3-4 exon V insertion in fig 1A) that knocked out LOX3 gene expression (see page 923 in figure 1D) by deleting the message after the Mu insertion point in exon V and truncated the encoded LOX3 protein open reading frame that resulted in increased resistance to stem rot and root rot as a reduction of the disease severity upon F. verticillioides, Colletotrichum graminicola, and Cochliobolus heterostrophus infections (see page 928 in figure 6A and 6B; and page 929 sentence spanning left and right column). In addition, figure 1 shows the Mu insertion site in exon V of the ZmLOX3 gene; wherein the Mu element insertion into the endogenous ZmLOX3 gene is at least one base insertion and the editing system and a nucleic acid binding domain thereof are not structural features of the maize plant or plant cell comprising a mutation in a ZmLOX3 gene. Further an alignment of SEQ ID NO: 79 (the coding sequence for LOX3 shown below) and SEQ ID NO: 94 of claim 15 shows that exon V of SEQ ID NO: 94 (indicated) is within the LOX3 coding region of SQ ID NO: 79.
Title: US-17-995-483-79_f1_t2595
Perfect score: 2595
Sequence: 1 atgctgagcgggatcatcga..........ccaacagcatctccatctga 2595
Scoring table: IDENTITY_NUC
Gapop 10.0 , Gapext 1.0
Searched: 1 seqs, 8509 residues
Total number of hits satisfying chosen parameters: 2
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 2 summaries
Database : US-17-995-483-94_f1_t8509.seq:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 1671.4 64.4 8509 1 US-17-995-483-94_f1_t850
c 2 70.8 2.7 8509 1 US-17-995-483-94_f1_t850
ALIGNMENTS
RESULT 1
US-17-995-483-94_f1_t8509
Query Match 64.4%; Score 1671.4; DB 1; Length 8509;
Best Local Similarity 84.0%;
Matches 2113; Conservative 0; Mismatches 1; Indels 401; Gaps 4;
Qy 482 ATACGTACCTGCCAAGCCAGATGCCGGCGGCGCTGAAGCCGTACCGCGACGACGAGCTCC 541
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3995 AGACGTACCTGCCAAGCCAGATGCCGGCGGCGCTGAAGCCGTACCGCGACGACGAGCTCC 4054
Qy 542 GCAACCTCCGCGGCGACGACCAGCAGGGCCCCTACCAGGAGCACGACCGCGTGTACCGCT 601
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4055 GCAACCTCCGCGGCGACGACCAGCAGGGCCCCTACCAGGAGCACGACCGCGTGTACCGCT 4114
Qy 602 ACGACGTCTACAACGACCTCGGCGAGCCCGACGGCGGCAACCCGCGCCCCATCCTCGGCG 661
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4115 ACGACGTCTACAACGACCTCGGCGAGCCCGACGGCGGCAACCCGCGCCCCATCCTCGGCG 4174
Qy 662 GCTCCGCCGACCACCCGTACCCGCGCCGCTGCCGCACGGGCCGCAAGCCCACCAAAACC- 720
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4175 GCTCCGCCGACCACCCGTACCCGCGCCGCTGCCGCACGGGCCGCAAGCCCACCAAAACCG 4234
Qy 721 ------------------------------------------------------------ 720
Db 4235 GTGCGTGCGCCGTGCGCGGCTCTTCTATCTTCTCGGACGCAACATTTGCTGCAGGGCAGA 4294
Qy 721 ----------------------------------GACCCCAACTCGGAGAGCCGACTGTC 746
||||||||||||||||||||||||||
Db 4295 GAGGTTGTTGACGCTGACCTGTGACCGCATCGCAGACCCCAACTCGGAGAGCCGACTGTC 4354
Qy 747 GCTGGTGGAGCAGATCTACGTGCCGCGGGACGAGCGCTTCGGCCACCTCAAGATGTCCGA 806
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4355 GCTGGTGGAGCAGATCTACGTGCCGCGGGACGAGCGCTTCGGCCACCTCAAGATGTCCGA 4414
Qy 807 CTTCCTGGGCTACTCCATCAAGGCCATCACGCAGGGCATCATCCCGGCGGTGCGCACGTA 866
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4415 CTTCCTGGGCTACTCCATCAAGGCCATCACGCAGGGCATCATCCCGGCGGTGCGCACGTA 4474
Qy 867 CGTGGACACCACCCCGGGCGAGTTCGACTCCTTCCAGGACATCATCAACCTGTACGAGGG 926
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4475 CGTGGACACCACCCCGGGCGAGTTCGACTCCTTCCAGGACATCATCAACCTGTACGAGGG 4534
Qy 927 CGGGATCAAGCTGCCCAAGATCCAGGCGCTCGAGGACATGCGCAAGCTCTTCCCGCTCCA 986
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4535 CGGGATCAAGCTGCCCAAGATCCAGGCGCTCGAGGACATGCGCAAGCTCTTCCCGCTCCA 4594
Qy 987 GCTCGTCAAGGACCTCCTCCCCGCCGGCGGGGACTACCTGCTCAAGCTCCCCATCCCACA 1046
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4595 GCTCGTCAAGGACCTCCTCCCCGCCGGCGGGGACTACCTGCTCAAGCTCCCCATCCCACA 4654
Qy 1047 GATCATCCA--------------------------------------------------- 1055
|||||||||
Db 4655 GATCATCCAAGGCACGTCACGTATACCGATCGATGTCAGGGGCCGGCTGTTGTCTGGTCT 4714
Qy 1056 ---------------------------------------***-exon-5---[Wingdings font/0xE0]AGAGGA 1061
||||||
Db 4715 GCATATATATATGTGCTCCTATGGTTAACTGTGACTGCGTACGTTTCGCGGAACAGAGGA 4774
Qy 1062 CAAGAACGCGTGGAGGACCGACGAGGAGTTCGCGCGGGAGGTGCTCGCCGGCGTCAACCC 1121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4775 CAAGAACGCGTGGAGGACCGACGAGGAGTTCGCGCGGGAGGTGCTCGCCGGCGTCAACCC 4834
Qy 1122 GATGGTGATCACGCGCCTCAC--------------------------------------- 1142
|||||||||||||||||||||
Db 4835 GATGGTGATCACGCGCCTCACGGTGAGTCACTCACTTTGTGCAAAATGCGAGACCCGACC 4894
Qy 1143 ----------------------------------GGAGTTCCCGCCCAAGAGCACGCTGG 1168
||||||||||||||||||||||||||
Db 4895 CGAGACGGAATGTGCCTGACGCGCTCGATTTACAGGAGTTCCCGCCCAAGAGCACGCTGG 4954
Qy 1169 ACCCCAGCAAGTACGGCGACCACACCAGCACGATCACGGCGGAGCACATCGAGAAGAACC 1228
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4955 ACCCCAGCAAGTACGGCGACCACACCAGCACGATCACGGCGGAGCACATCGAGAAGAACC 5014
Qy 1229 TCGAGGGCCTCACGGTGCAGCAGGCGCTGGACGGCAACAGGCTCTACATCCTGGACCACC 1288
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5015 TCGAGGGCCTCACGGTGCAGCAGGCGCTGGACGGCAACAGGCTCTACATCCTGGACCACC 5074
Qy 1289 ACGACCGCTTCATGCCGTTCCTCATCGACGTCAACAACCTGGAGGGCAACTTCATCTACG 1348
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5075 ACGACCGCTTCATGCCGTTCCTCATCGACGTCAACAACCTGGAGGGCAACTTCATCTACG 5134
Qy 1349 CCACCAGGACGCTCTTCTTCCTGCGCGGCGACGGCAGGCTCGCGCCCCTCGCCATCGAGC 1408
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5135 CCACCAGGACGCTCTTCTTCCTGCGCGGCGACGGCAGGCTCGCGCCCCTCGCCATCGAGC 5194
Qy 1409 TCAGCGAGCCGTACATCGACGGGGACCTCACCGTGGCCAAGAGCAAGGTCTACACGCCGG 1468
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5195 TCAGCGAGCCGTACATCGACGGGGACCTCACCGTGGCCAAGAGCAAGGTCTACACGCCGG 5254
Qy 1469 CGTCCAGCGGCGTCGAGGCCTGGGTGTGGCAGCTCGCCAAGGCCTATGTCGCCGTCAACG 1528
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5255 CGTCCAGCGGCGTCGAGGCCTGGGTGTGGCAGCTCGCCAAGGCCTATGTCGCCGTCAACG 5314
Qy 1529 ACTCTGGCTGGCACCAACTCGTCAGCCACT------------------------------ 1558
||||||||||||||||||||||||||||||
Db 5315 ACTCTGGCTGGCACCAACTCGTCAGCCACTGGTACGTACGAAGAACTACAACTACTCCTA 5374
Qy 1559 ------------------------------------------------------------ 1558
Db 5375 TATATGTCCTATATGACAATGGCATCGCATCGTGTCATGTCTATGACATCGCCAAATGCA 5434
Qy 1559 --------------------------------------GGCTGAACACCCACGCGGTGAT 1580
||||||||||||||||||||||
Db 5435 TGCGTTGATGGTCATGATCTATTCTCTGCGTGCGTGCAGGCTGAACACCCACGCGGTGAT 5494
Qy 1581 GGAGCCGTTCGTGATCGCGACGAACCGGCAGCTGAGCGTGACGCACCCGGTGCACAAGCT 1640
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5495 GGAGCCGTTCGTGATCGCGACGAACCGGCAGCTGAGCGTGACGCACCCGGTGCACAAGCT 5554
Qy 1641 CCTGAGCTCGCACTTCCGCGACACCATGACCATCAACGCGCTGGCGCGGCAGACGCTCAT 1700
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5555 CCTGAGCTCGCACTTCCGCGACACCATGACCATCAACGCGCTGGCGCGGCAGACGCTCAT 5614
Qy 1701 CAACGGCGGCGGCATCTTCGAGATGACCGTCTTCCCGGGCAAGTACGCGCTGGGCATGTC 1760
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5615 CAACGGCGGCGGCATCTTCGAGATGACCGTCTTCCCGGGCAAGTACGCGCTGGGCATGTC 5674
Qy 1761 CTCCGTGGTGTACAAGAGCTGGAACTTCACCGAGCAGGGCCTCCCCGCCGACCTCGTCAA 1820
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5675 CTCCGTGGTGTACAAGAGCTGGAACTTCACCGAGCAGGGCCTCCCCGCCGACCTCGTCAA 5734
Qy 1821 GAGGGGCGTGGCGGTGGCGGACCCGTCCAGCCCGTACAAGGTGCGGCTGCTGATCGAGGA 1880
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5735 GAGGGGCGTGGCGGTGGCGGACCCGTCCAGCCCGTACAAGGTGCGGCTGCTGATCGAGGA 5794
Qy 1881 CTACCCGTACGCGAGCGACGGGCTGGCCATCTGGCACGCCATCGAGCAGTGGGTGGGCGA 1940
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5795 CTACCCGTACGCGAGCGACGGGCTGGCCATCTGGCACGCCATCGAGCAGTGGGTGGGCGA 5854
Qy 1941 GTACCTGGCCATCTACTACCCCGACGACGGCGCGCTGCGGGGCGACGAGGAGCTGCAGGC 2000
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5855 GTACCTGGCCATCTACTACCCCGACGACGGCGCGCTGCGGGGCGACGAGGAGCTGCAGGC 5914
Qy 2001 GTGGTGGAAGGAGGTGCGCGAGGTCGGGCACGGCGACCACAAGGACGCGCCCTGGTGGCC 2060
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5915 GTGGTGGAAGGAGGTGCGCGAGGTCGGGCACGGCGACCACAAGGACGCGCCCTGGTGGCC 5974
Qy 2061 CAAGATGCAGGCCGTGTCGGAGCTCGCCAGCGCCTGCACCACCATCATCTGGATCGCGTC 2120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 5975 CAAGATGCAGGCCGTGTCGGAGCTCGCCAGCGCCTGCACCACCATCATCTGGATCGCGTC 6034
Qy 2121 GGCGCTCCACGCCGCCGTCAACTTCGGCCAGTACCCGTACGCGGGGTACCTCCCGAACAG 2180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6035 GGCGCTCCACGCCGCCGTCAACTTCGGCCAGTACCCGTACGCGGGGTACCTCCCGAACAG 6094
Qy 2181 GCCCACGGTGAGCCGGCGCCGGATGCCGGAGCCCGGCAGCAAGGAGTACGAGGAGCTGGA 2240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6095 GCCCACGGTGAGCCGGCGCCGGATGCCGGAGCCCGGCAGCAAGGAGTACGAGGAGCTGGA 6154
Qy 2241 GCGCGACCCGGAGCGCGGCTTCATCCACACCATCACGAGCCAGATCCAGACCATCATCGG 2300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6155 GCGCGACCCGGAGCGCGGCTTCATCCACACCATCACGAGCCAGATCCAGACCATCATCGG 6214
Qy 2301 CATCTCGCTCATCGAGATCCTCTCCAAGCACTCCTCCGACGAGGTGTACCTCGGCCAGCG 2360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6215 CATCTCGCTCATCGAGATCCTCTCCAAGCACTCCTCCGACGAGGTGTACCTCGGCCAGCG 6274
Qy 2361 CGACACCCCCGAGTGGACCTCCGACGCCCGGGCGCTGGCGGCGTTCAAGAGGTTCAGCGA 2420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6275 CGACACCCCCGAGTGGACCTCCGACGCCCGGGCGCTGGCGGCGTTCAAGAGGTTCAGCGA 6334
Qy 2421 CGCGCTGGTCAAGATCGAGGGCAAGGTGGTGGGCGAGAACCGCGACCCGCAGCTGAGGAA 2480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6335 CGCGCTGGTCAAGATCGAGGGCAAGGTGGTGGGCGAGAACCGCGACCCGCAGCTGAGGAA 6394
Qy 2481 CAGGAACGGCCCCGCCGAGTTCCCCTACATGCTGCTCTATCCCAACACCTCTGACCACAG 2540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6395 CAGGAACGGCCCCGCCGAGTTCCCCTACATGCTGCTCTATCCCAACACCTCTGACCACAG 6454
Qy 2541 TGGCGCCGCCGCAGGGCTCACTGCCAAGGGCATCCCCAACAGCATCTCCATCTGA 2595
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 6455 TGGCGCCGCCGCAGGGCTCACTGCCAAGGGCATCCCCAACAGCATCTCCATCTGA 6509
Although the GAO reference did not explicitly teach the sequence of the ZmLOX3 gene, support for the lipoxygenase taught in GAO (2007) Molecular Plant-Microbe Interactions 20(8): 922-933 being a lipoxygenase encoded by the ZmLox3 lipoxygenase gene is found in Gao (2008) Molecular Plant-Microbe Interactions, 21 (1): 98-109 on page 99 in Results section first paragraph spanning the left and right column, where the lox3-4 mutant having an exonic Mu insertion into ZmLox3 completely suppressed expression of ZmLox3; and further in the paragraph in the right column the "ccsap92" taught by Wilson (2001) is ZmLOX3; and thus the Mu insertion mutant (ZmLox3-4) of Gao (2007) is into the ccsap92 of Wilson (2001) Molecular Plant-Microbe Interactions; Vol. 14, no. 8; pp.980-987 (see sequence search result immediately below); which reads upon the instantly claimed LOX3 sequences of the instant claims namely SEQ ID NO: 78-80; and thus Gao (2007) anticipates instant claims 1, 7, 8, 15, 22, 24, 30 and 34. Moreover, contrary to assertions in Applicants remarks filed 11/05/2025, support for Gao (2007) is found in the above references and information from the search alignment below teaching the sequence identity of ZmLOX3 with respect to earlier designation of ZmLOX3 i.e. the "ccsap92" taught by Wilson (2001).
RESULT 1 US-17-995-483-80 (1-864) x AF329371 (1-2595)
AF329371
LOCUS AF329371 2595 bp mRNA linear PLN 01-FEB-2013
DEFINITION Zea mays lipoxygenase mRNA, complete cds.
ACCESSION AF329371
VERSION AF329371.1
KEYWORDS .
SOURCE Zea mays
ORGANISM Zea mays
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD
clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae;
Zea.
REFERENCE 1 (bases 1 to 2595)
AUTHORS Wilson,R.A., Gardner,H.W. and Keller,N.P.
TITLE Cultivar-dependent expression of a maize lipoxygenase responsive to
seed infesting fungi
JOURNAL Mol. Plant Microbe Interact. 14 (8), 980-987 (2001)
PUBMED 11497470
REFERENCE 2 (bases 1 to 2595)
AUTHORS Wilson,R.A., Maddox,J., Duvick,J. and Keller,N.P.
TITLE Direct Submission
JOURNAL Submitted (14-DEC-2000) Plant Pathology and Microbiology, Texas A&M
University, TAMUS 2132, College Station, TX 77843, USA
FEATURES Location/Qualifiers
source 1..2595
/organism="Zea mays"
/mol_type="mRNA"
/db_xref="taxon:4577"
CDS 1..2595
/codon_start=1
/product="lipoxygenase"
/protein_id="AAG61118.1"
/translation="MLSGIIDGLTGANKHARLKGTVVLMRKNVLDLNDFGATVVDSIS
EFLGKGVTCQLISSTLVDANNGNRGRVGAEANLEQWLTSLPSLTTGESKFGVTFDWEV
EKLGVPGAVVVKNNHAAEFFLKTITLDDVPGRGAVTFVANSWVYPAGKYRYNRVFFSN
DTYLPSQMPAALKPYRDDELRNLRGDDQQGPYQEHDRVYRYDVYNDLGEPDGGNPRPI
LGGSADHPYPRRCRTGRKPTKTDPNSDSRLSLVEQIYVPRDERFGHLKMSDFLGYSIK
AITQGIIPAVRTYVDTTPGEFDSFQDIINLYEGGIKLPKIQALEDMRKLFPLQLVKDL
LPAGGDYLLKLPIPQIIQEDKNAWRTDEEFAREVLAGVNPMVITRLTEFPPKSTLDPS
KYGDHTSTITAEHIEKNLEGLTVQQALDGNRLYILDHHDRFMPFLIDVNNLEGNFIYA
TRTLFFLRGDGRLAPLAIELSEPYIDGDLTVAKSKVYTPASSGVEAWVWQLAKAYVAV
NDSGWHQLVSHWLNTHAVMEPFVIATNRQLSVTHPVHKLLSSHFRDTMTINALARQTL
INGGGIFEMTVFPGKYALGMSSVVYKSWNFTEQGLPADLVKRGVAVADPSSPYKVRLL
IEDYPYASDGLAIWHAIEQWVGEYLAIYYPDDGALRGDEELQAWWKEVREVGHGDHKD
APWWPKMQAVSELASACTTIIWIASALHAAVNFGQYPYAGYLPNRPTVSRRRMPEPGS
KEYEELERDPERGFIHTITSQIQTIIGISLIEILSKHSSDEVYLGQRDTPEWTSDARA
LAAFKRFSDALVKIEGKVVGENRDPQLRNRNGPAEFPYMLLYPNTSDHSGAAAGLTAK
GIPNSISI
Alignment Scores:
Length: 2595
Score: 4558.00 Matches: 863
Percent Similarity: 100.0% Conservative: 1
Best Local Similarity: 99.9% Mismatches: 0
Query Match: 99.9% Indels: 0
Gaps: 0
US-17-995-483-80 (1-864) x AF329371 (1-2595)
Qy 1 MetLeuSerGlyIleIleAspGlyLeuThrGlyAlaAsnLysHisAlaArgLeuLysGly 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGCTGAGCGGGATCATCGACGGGCTGACGGGGGCGAACAAGCATGCGCGGCTCAAGGGC 60
Qy 21 ThrValValLeuMetArgLysAsnValLeuAspLeuAsnAspPheGlyAlaThrValVal 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ACGGTGGTGCTCATGCGCAAGAACGTGCTGGACCTCAACGACTTCGGCGCCACCGTCGTT 120
Qy 41 AspSerIleSerGluPheLeuGlyLysGlyValThrCysGlnLeuIleSerSerThrLeu 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GACAGCATCAGCGAGTTCCTCGGCAAGGGGGTCACCTGCCAGCTCATCAGCTCCACCCTC 180
Qy 61 ValAspAlaAsnAsnGlyAsnArgGlyArgValGlyAlaGluAlaAsnLeuGluGlnTrp 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GTCGACGCCAACAACGGCAACCGCGGGCGGGTCGGGGCGGAGGCGAACCTGGAGCAGTGG 240
Qy 81 LeuThrSerLeuProSerLeuThrThrGlyGluSerLysPheGlyValThrPheAspTrp 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CTGACGAGCCTGCCGTCGCTGACGACCGGCGAGTCCAAGTTCGGCGTCACGTTCGACTGG 300
Qy 101 GluValGluLysLeuGlyValProGlyAlaValValValLysAsnAsnHisAlaAlaGlu 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GAGGTGGAGAAGCTGGGAGTGCCGGGGGCCGTCGTCGTCAAGAACAACCACGCCGCCGAG 360
Qy 121 PhePheLeuLysThrIleThrLeuAspAspValProGlyArgGlyAlaValThrPheVal 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 TTCTTCCTCAAGACAATCACCCTCGACGACGTGCCCGGCCGCGGCGCCGTCACCTTCGTC 420
Qy 141 AlaAsnSerTrpValTyrProAlaGlyLysTyrArgTyrAsnArgValPhePheSerAsn 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GCCAACTCCTGGGTCTACCCCGCGGGCAAGTACCGCTACAACCGCGTCTTCTTCTCCAAC 480
Qy 161 AspThrTyrLeuProSerGlnMetProAlaAlaLeuLysProTyrArgAspAspGluLeu 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GATACGTACCTGCCAAGCCAGATGCCGGCGGCGCTGAAGCCGTACCGCGACGACGAGCTC 540
Qy 181 ArgAsnLeuArgGlyAspAspGlnGlnGlyProTyrGlnGluHisAspArgValTyrArg 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 CGCAACCTCCGCGGCGACGACCAGCAGGGCCCCTACCAGGAGCACGACCGCGTGTACCGC 600
Qy 201 TyrAspValTyrAsnAspLeuGlyGluProAspGlyGlyAsnProArgProIleLeuGly 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 TACGACGTCTACAACGACCTCGGCGAGCCCGACGGCGGCAACCCGCGCCCCATCCTCGGC 660
Qy 221 GlySerAlaAspHisProTyrProArgArgCysArgThrGlyArgLysProThrLysThr 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 GGCTCCGCCGACCACCCGTACCCGCGCCGCTGCCGCACGGGCCGCAAGCCCACCAAAACC 720
Qy 241 AspProAsnSerGluSerArgLeuSerLeuValGluGlnIleTyrValProArgAspGlu 260
||||||||||||:::|||||||||||||||||||||||||||||||||||||||||||||
Db 721 GACCCCAACTCGGATAGCCGACTGTCGCTGGTGGAGCAGATCTACGTGCCGCGGGACGAG 780
Qy 261 ArgPheGlyHisLeuLysMetSerAspPheLeuGlyTyrSerIleLysAlaIleThrGln 280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CGCTTCGGCCACCTCAAGATGTCCGACTTCCTGGGCTACTCCATCAAGGCCATCACGCAG 840
Qy 281 GlyIleIleProAlaValArgThrTyrValAspThrThrProGlyGluPheAspSerPhe 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 GGCATCATCCCGGCGGTGCGCACGTACGTGGACACCACCCCGGGCGAGTTCGACTCCTTC 900
Qy 301 GlnAspIleIleAsnLeuTyrGluGlyGlyIleLysLeuProLysIleGlnAlaLeuGlu 320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 CAGGACATCATCAACCTGTACGAGGGCGGGATCAAGCTGCCCAAGATCCAGGCGCTCGAG 960
Qy 321 AspMetArgLysLeuPheProLeuGlnLeuValLysAspLeuLeuProAlaGlyGlyAsp 340
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GACATGCGCAAGCTCTTCCCGCTCCAGCTCGTCAAGGACCTCCTCCCCGCCGGCGGGGAC 1020
Qy 341 TyrLeuLeuLysLeuProIleProGlnIleIleGlnGluAspLysAsnAlaTrpArgThr 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 TACCTGCTCAAGCTCCCCATCCCACAGATCATCCAAGAGGACAAGAACGCGTGGAGGACC 1080
Qy 361 AspGluGluPheAlaArgGluValLeuAlaGlyValAsnProMetValIleThrArgLeu 380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 GACGAGGAGTTCGCGCGGGAGGTGCTCGCCGGCGTCAACCCGATGGTGATCACGCGCCTC 1140
Qy 381 ThrGluPheProProLysSerThrLeuAspProSerLysTyrGlyAspHisThrSerThr 400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 ACGGAGTTCCCGCCCAAGAGCACGCTGGACCCCAGCAAGTACGGCGACCACACCAGCACG 1200
Qy 401 IleThrAlaGluHisIleGluLysAsnLeuGluGlyLeuThrValGlnGlnAlaLeuAsp 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1201 ATCACGGCGGAGCACATCGAGAAGAACCTCGAGGGCCTCACGGTGCAGCAGGCGCTGGAC 1260
Qy 421 GlyAsnArgLeuTyrIleLeuAspHisHisAspArgPheMetProPheLeuIleAspVal 440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1261 GGCAACAGGCTCTACATCCTGGACCACCACGACCGCTTCATGCCGTTCCTCATCGACGTC 1320
Qy 441 AsnAsnLeuGluGlyAsnPheIleTyrAlaThrArgThrLeuPhePheLeuArgGlyAsp 460
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1321 AACAACCTGGAGGGCAACTTCATCTACGCCACCAGGACGCTCTTCTTCCTGCGCGGCGAC 1380
Qy 461 GlyArgLeuAlaProLeuAlaIleGluLeuSerGluProTyrIleAspGlyAspLeuThr 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1381 GGCAGGCTCGCGCCCCTCGCCATCGAGCTCAGCGAGCCGTACATCGACGGGGACCTCACC 1440
Qy 481 ValAlaLysSerLysValTyrThrProAlaSerSerGlyValGluAlaTrpValTrpGln 500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1441 GTGGCCAAGAGCAAGGTCTACACGCCGGCGTCCAGCGGCGTCGAGGCCTGGGTGTGGCAG 1500
Qy 501 LeuAlaLysAlaTyrValAlaValAsnAspSerGlyTrpHisGlnLeuValSerHisTrp 520
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1501 CTCGCCAAGGCCTATGTCGCCGTCAACGACTCTGGCTGGCACCAACTCGTCAGCCACTGG 1560
Qy 521 LeuAsnThrHisAlaValMetGluProPheValIleAlaThrAsnArgGlnLeuSerVal 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1561 CTGAACACCCACGCGGTGATGGAGCCGTTCGTGATCGCGACGAACCGGCAGCTGAGCGTG 1620
Qy 541 ThrHisProValHisLysLeuLeuSerSerHisPheArgAspThrMetThrIleAsnAla 560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1621 ACGCACCCGGTGCACAAGCTCCTGAGCTCGCACTTCCGCGACACCATGACCATCAACGCG 1680
Qy 561 LeuAlaArgGlnThrLeuIleAsnGlyGlyGlyIlePheGluMetThrValPheProGly 580
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1681 CTGGCGCGGCAGACGCTCATCAACGGCGGCGGCATCTTCGAGATGACCGTCTTCCCGGGC 1740
Qy 581 LysTyrAlaLeuGlyMetSerSerValValTyrLysSerTrpAsnPheThrGluGlnGly 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1741 AAGTACGCGCTGGGCATGTCCTCCGTGGTGTACAAGAGCTGGAACTTCACCGAGCAGGGC 1800
Qy 601 LeuProAlaAspLeuValLysArgGlyValAlaValAlaAspProSerSerProTyrLys 620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1801 CTCCCCGCCGACCTCGTCAAGAGGGGCGTGGCGGTGGCGGACCCGTCCAGCCCGTACAAG 1860
Qy 621 ValArgLeuLeuIleGluAspTyrProTyrAlaSerAspGlyLeuAlaIleTrpHisAla 640
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1861 GTGCGGCTGCTGATCGAGGACTACCCGTACGCGAGCGACGGGCTGGCCATCTGGCACGCC 1920
Qy 641 IleGluGlnTrpValGlyGluTyrLeuAlaIleTyrTyrProAspAspGlyAlaLeuArg 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1921 ATCGAGCAGTGGGTGGGCGAGTACCTGGCCATCTACTACCCCGACGACGGCGCGCTGCGG 1980
Qy 661 GlyAspGluGluLeuGlnAlaTrpTrpLysGluValArgGluValGlyHisGlyAspHis 680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1981 GGCGACGAGGAGCTGCAGGCGTGGTGGAAGGAGGTGCGCGAGGTCGGGCACGGCGACCAC 2040
Qy 681 LysAspAlaProTrpTrpProLysMetGlnAlaValSerGluLeuAlaSerAlaCysThr 700
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2041 AAGGACGCGCCCTGGTGGCCCAAGATGCAGGCCGTGTCGGAGCTCGCCAGCGCCTGCACC 2100
Qy 701 ThrIleIleTrpIleAlaSerAlaLeuHisAlaAlaValAsnPheGlyGlnTyrProTyr 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2101 ACCATCATCTGGATCGCGTCGGCGCTCCACGCCGCCGTCAACTTCGGCCAGTACCCGTAC 2160
Qy 721 AlaGlyTyrLeuProAsnArgProThrValSerArgArgArgMetProGluProGlySer 740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2161 GCGGGGTACCTCCCGAACAGGCCCACGGTGAGCCGGCGCCGGATGCCGGAGCCCGGCAGC 2220
Qy 741 LysGluTyrGluGluLeuGluArgAspProGluArgGlyPheIleHisThrIleThrSer 760
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2221 AAGGAGTACGAGGAGCTGGAGCGCGACCCGGAGCGCGGCTTCATCCACACCATCACGAGC 2280
Qy 761 GlnIleGlnThrIleIleGlyIleSerLeuIleGluIleLeuSerLysHisSerSerAsp 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2281 CAGATCCAGACCATCATCGGCATCTCGCTCATCGAGATCCTCTCCAAGCACTCCTCCGAC 2340
Qy 781 GluValTyrLeuGlyGlnArgAspThrProGluTrpThrSerAspAlaArgAlaLeuAla 800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2341 GAGGTGTACCTCGGCCAGCGCGACACCCCCGAGTGGACCTCCGACGCCCGGGCGCTGGCG 2400
Qy 801 AlaPheLysArgPheSerAspAlaLeuValLysIleGluGlyLysValValGlyGluAsn 820
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2401 GCGTTCAAGAGGTTCAGCGACGCGCTGGTCAAGATCGAGGGCAAGGTGGTGGGCGAGAAC 2460
Qy 821 ArgAspProGlnLeuArgAsnArgAsnGlyProAlaGluPheProTyrMetLeuLeuTyr 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2461 CGCGACCCGCAGCTGAGGAACAGGAACGGCCCCGCCGAGTTCCCCTACATGCTGCTCTAT 2520
Qy 841 ProAsnThrSerAspHisSerGlyAlaAlaAlaGlyLeuThrAlaLysGlyIleProAsn 860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2521 CCCAACACCTCTGACCACAGTGGCGCCGCCGCAGGGCTCACTGCCAAGGGCATCCCCAAC 2580
Qy 861 SerIleSerIle 864
||||||||||||
Db 2581 AGCATCTCCATC 2592
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 12, 50, 56-57, 60-62 and 84-86 are rejected under 35 U.S.C. 103 as being unpatentable over Gao, X. et al., MPMI (2007) Vol. 20, No. 8; pp. 922-933 in view of Gao, X. et al. (2008) Planta 227:491-503 and in further view of Agarwal, A. et al., Physiol. Mol Biol Plants (April 2018) 24(2): pp. 175-183 and U.S. Patent 6921847.
Claims 1, 7, 8, 15, 22, 24, 30 and 34 are rejected supra under 35 U.S.C. 102(a)(1) as being clearly anticipated by Gao, X. et al., MPMI (2007) Vol. 20, No. 8; pp. 922-933 in light of Gao (2008) Molecular Plant-Microbe Interactions, 21 (1): 98-109; and Wilson (2001) Molecular Plant-Microbe Interactions; Vol. 14, no. 8; pp. 980-987.
The claims are broadly drawn to a maize plant or plant cell having a mutation in at least one or two different endogenous LOX genes encoding a LOX protein; wherein the mutation is in at least one LOX gene having at least 90% identity to a LOX polynucleotide sequence of SEQ ID NO: 72, 75, 78, or 81; or 90% thereof; or encodes a polypeptide having the amino acid sequence of SEQ ID NO: 74, 77, 80, or 83; or 95% thereof; or the LOX polynucleotide of 73, 76, 79, or 82 or 90% thereof; or wherein the mutated LOX gene comprises a nucleotide sequence of SEQ ID NO: 94, 96, 97-105, or 106; and wherein the plant acquires resistance to ear rot or stalk rot.
Claims 12, 50, 56, 57, 60-62 and 84-86 are drawn to maize plants having one or two mutations including deletions or truncations in the ZmLOX genes of the instant claims that either reduce or knockout LOX gene expression and that reduce severity of F. verticillioides, Colletotrichum graminicola, and Cochliobolus heterostrophus infections for example and also includes the methodology of endonuclease cleavage using a binding domain directed to a specific target site for making deletions and/or truncations.
Gao (2007) teaches the inactivation of maize LOX3 by insertion of a Mu transposable element led to a reduction of the disease severity upon F. verticillioides, Colletotrichum graminicola, and Cochliobolus heterostrophus infections (see rejection under 102 above and Abstract).
Gao (2007) does not teach the physiological role of any other LOX genes from maize or a deletion mutation therein other than the physiological role of ZmLOX3 and Mu deletion mutation into ZmLOX3.
Gao (2008) teaches LOX6 is more likely to contribute to disease development rather than defense response and is very similar to LOX3 in that regard because it was induced by a fungal leaf rot pathogen Cochliobolus carbonum during compatible interactions and suggested that ZmLOX6 may contribute to susceptibility to this pathogen; Gao also teaches that Mu insertion mutants of ZmLOX6 have been made to further study the physiological role of ZmLOX6 (see Abstract and page 501 paragraph spanning left and right columns and final paragraph of right column).
Neither of the two Gao references above teach a CRISPR method for genetic engineering of LOX in maize to improve resistance to rot.
Agarwal (2018) teaches a summary of the recent advances of targeted genome engineering in maize; and that successful engineering of maize genes for crop improvement using CRISPR can obviate many regulatory hurdles and that the current state of the art in maize transformation using CRISPR can mitigate off target effects (See Abstract, page 178 in Table 1, and pages 180-182).
U.S. Patent 6921847 teaches ZmLOX6 (SEQ ID NO: 25) sequences having 100% sequence identity to the instantly claimed LOX6 coding sequence of SEQ ID NO: 82; methods for making deletions and truncations were common in the art at the time of the instant filing (see section spanning columns 11 and 12 from line 66 in column 11 to line 10 of column 12); and the ‘847 Patent teaches antisense inhibition of ZmLOX6 in maize in claim 5 and a method for enhancing a plant defense response in claim 14.
It would have been obvious at the time of the instant filing to knock out expression of ZmLOX6 gene in maize as taught by the ‘847 Patent for further study as suggested by Gao (2008), and to also further include the knockout maize mutant of ZmLOX3 gene expression in the same maize plant since they have both been identified as disease susceptibility factors in maize by Gao (2008); and combining deletion mutations of two known susceptibility factors and reducing or eliminating rot in maize is an obvious strategy to improve maize growth and yield.
One of ordinary skill would have been motivated by the need in the art of maize cultivation to eliminate the problem of root rot and leaf rot from maize crops and would have appreciated the success of Gao in identifying ZmLOX3 and ZmLOX6 as susceptibility factors in both root rot and leaf rot and appreciated the success of Gao (2007) in eliminating susceptibility in the ZmLOX3-4 mutant and the success of the ‘847 Patent in enhancing plant defense response (claim 14 of the ‘847 Patent).
Moreover, one of ordinary skill would have understood that the level of genetic engineering of specific genes in a targeted fashion in maize using CRISPR as taught by Agarwal would allow for the development of a value added trait of great value to the commercial market by combining a knockout of both ZmLOX3 and ZmLOX6; and one of ordinary skill would have a reasonable expectation of success given the success of Gao in elucidating the roles of LOX3 and LOX6 in maize, and the level of practice in the art whereby the art had successfully made modifications to LOX3 and LOX6 that reduced root rot and enhanced plant defense response.
In addition, with respect to instant claims 56-57, 60-62, and 84-86, the in frame or out of frame deletion and the size and/or location of the deletion within the ZmLOX3 and ZmLOX6 genes are features that would flow from making a rational choice to achieve the desired effect such features as targeting a catalytic amino acid residue thereby eliminating activity or truncating the protein close to the 5’ end of the polypeptide thereby increasing the probability of a complete knockout of the LOX activity whereby elimination of two maize rot susceptibility factors such as ZmLOX3 and ZmLOX6 without introducing any foreign DNA into the maize plant or plant cell is an achievable goal in the art of maize genetic engineering.
Claims 1, 7, 8, 12, 15, 22, 24, 30, 34, 50, 56-57, 60-62 and 84-86 are rejected.
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/RUSSELL KALLIS/Primary Examiner, Art Unit 1663