DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 21-45 are canceled.
Claims 1-20 are pending.
Claims 1-20 are examined herein.
Claims 1-20 are rejected.
Priority
Application No. 18/282,693 filed on 09/18/2023 is a 371 of PCT Application No. PCT/US22/22271 filed on 03/29/2022, which claims priority to provisional Application No. 63/169,316 filed on 04/01/2021.
Restriction/ Election
In view of Applicant’s cancellation of claims 21-45, the previous restriction requirement as set forth in the Office action mailed on 10/30/2025 is hereby withdrawn.
Claim Objections
In claim 1, “HI” is used as an abbreviation. It is suggested to
insert a definition for HI without bringing in new matter, immediately before the first
appearance of “HI” in claim 1; and to enclose the appearance of “HI” in
parentheses (in claim 1 only).
In claims 5 and 17, “TF” is used as an abbreviation. It is suggested to
insert a definition for TF without bringing in new matter, immediately before the first
appearance of “TF” in claim 1; and to enclose the appearance of “TF” in
parentheses (in claim 1 only).
Claim 12 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims (see closest prior art section below).
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 7, 9-12, and 19 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.
Claims 7 and 19 recite “wherein the at least one TF-QTL is qCYTO-ATF3.1 on chromosome 3 (TF-QTL qCYTO-A_TF3.1)”. qCYTO-ATF3.1 is not a term recognized in the prior art, and is not defined by the claims or specification. The specification provides markers that can be used to assist in identifying a qCYTO-ATF3.1 TF-QTL (p. 33, Table 6), however Table 21 identifies plant lines that are “favorable” that vary in presence/ absence of the markers described in Table 6. It is unclear which markers are required to have the SYB-INBC34 genotype according to Table 6, or what other mutations within or outside of the 6 described markers could constitute identification of a qCYTO-ATF3.1 TF-QTL. For at least these reasons, the metes and bounds of the claim are not clear. For purposes of examination, a qCYTO-ATF3.1 TF-QTL is broadly reasonably interpreted as a QTL on chromosome 3 that is associated with increased transformation.
Claim 9 recites “The maize plant of claim 8, wherein the maize plant is homozygous for a selectable marker” and depends from claim 8 which recites “The maize plant of claim 1, wherein the maize plant comprises a selectable marker”. It is unclear if the recitation of a selectable marker in claim 9 is the same selectable marker referenced in claim 8, or a different selectable marker. Applicant should clarify if it is the same selectable marker and if so, amend claim 9 to recite “The maize plant of claim 8, wherein the maize plant is homozygous for the selectable marker.”
Claims 10-12 are also rejected as a function of their dependency.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 17 and 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lowe (Lowe, B. A., Way, M. M., Kumpf, J. M., Rout, J., Warner, D., Johnson, R., ... & Chomet, P. S. (2006). Marker assisted breeding for transformability in maize. Molecular Breeding, 18(3), 229-239), and as evidenced by Allen (Allen, J. O., Fauron, C. M., Minx, P., Roark, L., Oddiraju, S., Lin, G. N., ... & Newton, K. J. (2007). Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics, 177(2), 1173-1192).
Claim 17 is drawn to a maize plant that is at least heterozygous for a TF allele at at least one quantitative trait locus (QTL) associated with increased transformation frequency (TF-QTL).
Claim 20 is drawn to the maize plant of claim 17, wherein the maize plant has a normal A ("NA") cytotype.
Regarding claim 17, Lowe discloses a paper about marker assisted breeding for transformability in maize, and specifically discloses maize plants having an A188-derived allele on chromosome 3 have high culturability and transformability (Table 2, p. 234, ¶1, p. 236, ¶2).
Regarding claim 20, Lowe discloses the A188-derived allele on chromosome 3 have high culturability and transformability (Table 2, p. 234, ¶1, p. 236, ¶2), therefore Lowe discloses A188 plants have a transformation frequency QTL that is located on chromosome 3. Maize line A188 has a normal A cytotype, as evidenced by Allen (See Materials and Methods: Mitochondrial DNA Preparation) (i.e. wherein the maize plant has a normal A cytotype).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-4, 8-10, and 13-16 are rejected under 35 U.S.C. 103 as being unpatentable over Que (US-20190136250-A1) and Chen (US-20180092316-A1).
Claim 1 is drawn to a maize plant homozygous for a loss-of-function mutation in the patatin-like phospholipase A2a gene (MATL) and at least heterozygous for a HI allele at at least one quantitative trait locus (QTL) associated with increased haploid induction (HI-QTL), wherein the maize plant has a normal A ("NA") cytotype.
Claim 2 is drawn to the maize plant of claim 1, wherein the maize plant is homozygous for the HI allele at the at least one HI-QTL.
Claim 3 is drawn to the maize plant of claim 1, wherein the at least one HI-QTL is qhir8 on chromosome 9 (HI-QTL ghir8).
Claim 4 is drawn to the maize plant of claim 3, wherein the HI allele at the HI-QTL ghir8 comprises a loss-of function mutation in the DUF679 domain membrane protein 7 (DMP) gene.
Claim 8 is drawn to the maize plant of claim 1, wherein the maize plant comprises a selectable marker.
Claim 9 is drawn to the maize plant of claim 8, wherein the maize plant is homozygous for a selectable marker.
Claim 10 is drawn to the maize plant of claim 9, wherein the selectable marker is any one of GUS, PMI, PAT, GFP, RFP, CFP, B1, CI, NPTII,HPT, ACC3, AADA, high oil content, R-navajo (R- nj), R1-scutellum (R1-SCM2), and/or an anthocyanin pigment.
Claim 13 is drawn to the maize plant of claim 1, wherein the maize plant is capable of expressing a DNA modification enzyme and optionally at least one guide nucleic acid.
Claim 14 is drawn to the maize plant of claim 13, wherein the DNA modification enzyme is a site- directed nuclease selected from the group consisting of Cas9 nuclease, Casl2a nuclease, meganucleases (MNs), zinc-finger nucleases, (ZFNs), transcription-activator like effector nucleases (TALENs), dCas9-Fokl, dCasl2a-FokI, chimeric Cas9-cytidine deaminase, chimeric Cas9-adenine deaminase, chimeric FENI-FokI, MegaTALs, a nickase Cas9 (nCas9), chimeric dCas9 non-Fokl nuclease, dCasl2a non-Fokl nuclease, chimeric Casl2a-cytidine deaminase, and Cas12a-adenine deaminase.
Claim 15 is drawn to the maize plant of claim 1, wherein the maize plant comprises one or more of a Non-Stiff Stalk germplasm, a Stiff Stalk germplasm, a Non-Stiff Stalk Iodent germplasm, a Non-Stiff Stalk Mo17-like germplasm, a Tropical germplasm, or a Subtropical germplasm.
Claim 16 is drawn to the maize plant of claim 1, wherein the maize plant is derived from any of lines Stock 6, RWK, RWS, UH400, AX5707RS, NP2222, SYN-INBE56, SYN-INBB23, SYN- INBF67, SYN-INBC34, SYN-INBD45, SYN-INBG78, SYN-INBH89, SYN-INBI90, SYN- INBJ13, and/or SYN-INBK14.
Regarding claim 1, Que teaches transforming the transformable line of maize called NP2222 (i.e. which has a normal A cytotype) with TALEN and CRISPR/Cas9 gene-editing machinery designed to target and knockout the maize PLA1/MATL gene located on chromosome 1, thereby resulting in a loss of function of MATL (¶0163). Que teaches the established lines that are homozygous for loss of function mutations in MATL are haploid inducer lines (¶0163).
Regarding claims 8-9, Que teaches the new NP2222-HI plants are homozygous wild-type for a color marker (i.e. the maize plant comprises a selectable marker and is homozygous for a selectable marker) (¶0157, 1066-0167).
Regarding claim 10, as described above, Que teaches the new NP2222-HI plants are homozygous wild-type for a color marker (¶0166-0167). In an alternative embodiment, Que further teaches the marker gene is selected from the group consisting of GUS, PMI, PAT, GFP, RFP, CFP, B 1, C1, R-nj, anthocyanin pigments, and any other marker gene (¶0157).
Regarding claims 13-14, Que teaches the NP2222-HI plant with the mutant version of MATL is stably transformed with Cas9+guide RNA to generate edits in targeted genes (¶0181-0189).
Regarding claims 15-16, Que teaches the maize plant is derived from NP2222 (i.e. a Non-Stiff Stalk Iodent germplasm, supported by ¶0176 of the instant specification) (¶0163).
However, Que does not explicitly teach:
the maize plant is also at least heterozygous for a HI allele at at least one quantitative trait locus (QTL) associated with increased haploid induction (HI-QTL) (remaining limitation of claim 1)
wherein the maize plant is homozygous for the HI allele at the at least one HI-QTL (claim 2)
wherein the at least one HI-QTL is qhir8 on chromosome 9 (HI-QTL ghir8) (claim 3)
wherein the HI allele at the HI-QTL ghir8 comprises a loss-of function mutation in the DUF679 domain membrane protein 7 (DMP) gene (claim 4)
Regarding the remaining limitation of claim 1, in analogous art, Chen teaches aside from qhir1 on chromosome 1, qhir8 is the other main QTL that can significantly improve haploid induction (¶0006). Chen teaches the gene associated with qhir8 is ZmDMP (encoding DUF679 DMP), and mutations to ZmDMP can greatly enhance haploid induction ability (¶0006). Chen teaches editing both the haploid inducing genes ZmPLA1 and ZmDMP (i.e. zmpla1-zmdmp) can quickly produce a haploid inducer line of high frequency, as compared to editing either gene alone (i.e. ZmPla1-zmdmp or zmpla1-ZmDMP) (¶0122).
Regarding claim 2, Chen teaches the generation of four types of maize: First is neither ZmPLA1 nor ZmDMP had mutations (i.e. wild-type or ZmPLA1-ZmDMP), second is homozygous mutations in the ZmDMP gene but no mutations in the ZmPLA1 gene (zmdmp-ZmPLA1), third is homozygous mutations in the ZmPLA1 gene but no mutations in the ZmDMP gene (zmpla1-ZmDMP), and fourth is mutations in both ZmPLA1 and ZmDMP gene (zmpla1-zmdmp) (¶0102). Because Chen teaches homozygous mutations in the genes and abbreviates the homozygous mutations with lowercase letters, the maize with mutations in both ZmPLA1 and ZmDMP gene (zmpla1-zmdmp) is reasonably interpreted to be homozygous for mutations in both ZmPLA1 and ZmDMP (i.e. wherein the plant is homozygous for the HI allele at the at least one HI-QTL).
Regarding claim 3, Chen teaches the HI-QTL is qhir8 on chromosome 9 (¶0006).
Regarding claim 4, Chen teaches the qhir8 QTL comprises a mutation in the DUF679 DMP gene that improves haploid induction ability (¶0006, 0096, 0122) (i.e. reasonably interpreted as a loss of function mutation).
It would therefore have been obvious to a person of ordinary skill in the art to modify the invention taught by Que to include the limitations of Chen to arrive at the instantly claimed method with a reasonable expectation of success because Chen teaches the NP222 line is highly transformable, therefore one of ordinary skill could edit the PLA1/MATL gene and the DMP gene as taught by Que and Chen without encountering any special technical obstacles and by doing so would have a reasonable expectation of success at generating a haploid inducer line. One having ordinary skill in the art would have been motivated to combine the teachings for the purpose of successfully introducing mutations into a maize plant for high haploid induction frequency because Que teaches the NP222 line (which has normal A cytotype) is highly transformable (¶0163), and Que teaches mutations to both PLA1/MATL and DMP genes increases overall haploid induction as compared to mutations of either gene alone (Table 2).
Claims 5-7 are rejected under 35 U.S.C. 103 as being unpatentable over Que and Chen as applied to claim 1 above, and further in view of Lowe (Lowe, B. A., Way, M. M., Kumpf, J. M., Rout, J., Warner, D., Johnson, R., ... & Chomet, P. S. (2006). Marker assisted breeding for transformability in maize. Molecular Breeding, 18(3), 229-239) and Salvo (Salvo, S., Cook, J., Carlson, A. R., Hirsch, C. N., Kaeppler, S. M., & Kaeppler, H. F. (2018). Genetic fine‐mapping of a quantitative trait locus (QTL) associated with embryogenic tissue culture response and plant regeneration ability in Maize (Zea mays L.). The Plant Genome, 11(2), 170111).
Claim 5 is drawn to the maize plant of claim 1, wherein the maize plant is at least heterozygous for a TF allele at at least one QTL associated with increased transformation frequency (TF- QTL).
Claim 6 is drawn to the maize plant of claim 5, wherein the maize plant is homozygous for the TF allele at the at least one TF-QTL.
Claim 7 is drawn to the maize plant of claim 6, wherein the at least one TF-QTL is qCYTO-A_TF3.1 on chromosome 3 (TF-QTL qCYTO-A_TF3.1).
Regarding claims 5-7, Que and Chen teach the limitations of claim 1 as set forth in the previous obviousness rejection. The teachings of Que and Chen as they are applied to claim 1 are set forth previously herein and are incorporated by reference.
However, Que and Chen do not explicitly teach:
wherein the maize plant is at least heterozygous for a TF allele at at least one QTL associated with increased transformation frequency (TF- QTL) (claim 5)
wherein the maize plant is homozygous for the TF allele at the at least one TF-QTL (claim 6)
wherein the at least one TF-QTL is qCYTO-A_TF3.1 on chromosome 3 (TF-QTL qCYTO-A_TF3.1) (claim 7)
In analogous art about marker assisted breeding for transformability in maize, Lowe teaches an A188-derived allele on chromosome 3 (from transformable A188 maize line) was associated with high culturability and transformability (Table 2, p. 234, ¶1, p. 236, ¶2). In other analogous art, Salvo supports the teaching of Lowe by further teaching isolines with large segments of homozygous A188 intervals in the putative QTL region on chromosome 3 are associated with higher regeneration of plantlets (Fig. 4, p. 8, ¶2).
It would therefore have been obvious to a person of ordinary skill in the art to modify the invention taught by Que and Chen to include the limitations of Lowe and Salvo to arrive at the instantly claimed method with a reasonable expectation of success because Lowe and Salvo teach introgression of the A188-derived allele at a QTL on chromosome 3 associated with high culturability and transformability (Table 2, p. 234, ¶1, p. 236, ¶2 of Lowe) and high plantlet regeneration (Fig. 4, p. 8, ¶2 of Salvo). One having ordinary skill in the art would have been motivated to combine the teachings to arrive at the instantly claimed methods for the purpose introgressing the specified allele on chromosome 3 to improve culturability, transformability, and regenerability of maize lines (Table 2, p. 234, ¶1, p. 236, ¶2 of Lowe, Fig. 4, p. 8, ¶2 of Salvo).
Claims 11 is rejected under 35 U.S.C. 103 as being unpatentable over Que and Chen as applied to claims 1 and 8-10 above, and further in view of Chintamanani (US-20180092316-A1).
Claim 11 is drawn to the maize plant of claim 10, wherein the maize plant is homozygous for the R1-scutellum (R1-SCM2) allele at the R1 locus on chromosome 10.
Regarding claim 11, Que and Chen teach the limitations of claims 1 and 8-10 as set forth in the previous obviousness rejection. The teachings of Que and Chen as they are applied to claims 1 and 8-10 are set forth previously herein and are incorporated by reference. Que also teaches the NP2222-HI plants are homozygous wild-type for a color marker (¶0157, 1066-0167).
However, Que and Chen do not explicitly teach wherein the maize plant is homozygous for the R1-scutellum (R1-SCM2) allele at the R1 locus on chromosome 10 (i.e. claim 11).
Regarding claim 11, in analogous art, Chintamanani teaches introgressing markers such as R1-scutellum2 (R1-Scm2) into the putative haploid inducer line can serve as evidence of the existence of the paternal genome in progeny indicating a diploid state, with absence indicating a haploid state. In other analogous art (¶0328). Additionally, because the R1 locus is located on chromosome 10, the introgression of R1-scutellum2 would occur at the R1 locus on chromosome 10.
It would therefore have been obvious to a person of ordinary skill in the art to modify the invention taught by Que and Chen to include the limitations of Chintamanani to arrive at the instantly claimed method with a reasonable expectation of success because Que teaches the maize plants are homozygous WT for a color marker that may be C1 (¶0157, 1066-0167), and Chintamanani teaches R1-Scm2 is another known color marker that can be introgressed into the haploid inducer plant used to assist in identifying haploid/ diploid state (¶0328). One having ordinary skill in the art would have been motivated to combine the teachings for the purpose expressing a visible color to identifying haploid/ diploid state (¶0328).
Claims 18-19 are rejected under 35 U.S.C. 103 as being unpatentable over Lowe as applied to claim 1 above, and further in view of Salvo (Salvo, S., Cook, J., Carlson, A. R., Hirsch, C. N., Kaeppler, S. M., & Kaeppler, H. F. (2018). Genetic fine‐mapping of a quantitative trait locus (QTL) associated with embryogenic tissue culture response and plant regeneration ability in Maize (Zea mays L.). The Plant Genome, 11(2), 170111.).
Claim 18 is drawn to the maize plant of claim 17, wherein the maize plant is homozygous for the TF allele at the at least one TF-QTL.
Claim 19 is drawn to the maize plant of claim 17, wherein the at least one TF-QTL is qCYTO-A_TF3.1 on chromosome 3 (TF-QTL qCYTO-A_TF3.1).
Regarding claims 18-19, Lowe teaches the limitations of claim 17 as set forth in the previous anticipation rejection. The teachings of Lowe as they are applied to claim 17 are set forth previously herein and are incorporated by reference.
However, Lowe does not explicitly teach:
wherein the maize plant is homozygous for the TF allele at the at least one TF-QTL (claim 18)
wherein the at least one TF-QTL is qCYTO-A_TF3.1 on chromosome 3 (TF-QTL qCYTO-A_TF3.1) (claim 19)
In analogous art, Salvo supports the teaching of Lowe by further teaching isolines with large segments of homozygous A188 intervals in the putative QTL region on chromosome 3 are associated with higher regeneration of plantlets (Fig. 4, p. 8, ¶2).
It would therefore have been obvious to a person of ordinary skill in the art to modify the invention taught by Lowe to include the limitations of Salvo to arrive at the instantly claimed method with a reasonable expectation of success because Lowe teaches introgression of the A188-derived allele at a QTL on chromosome 3 associated with high culturability and transformability (Table 2, p. 234, ¶1, p. 236, ¶2 of Lowe), and Salvo teaches plants homozygous for the A188 allele have high plantlet regeneration (Fig. 4, p. 8, ¶2 of Salvo). One having ordinary skill in the art would have been motivated to combine the teachings to arrive at the instantly claimed methods for the purpose of producing maize homozygous for the specified allele on chromosome 3 to improve culturability, transformability, and regenerability of maize lines (Table 2, p. 234, ¶1, p. 236, ¶2 of Lowe, Fig. 4, p. 8, ¶2 of Salvo).
Closest Prior Art
Claim 12 appears free of the prior art.
Regarding claim 12, the closest prior art is Que (US-20190136250-A1). Que teaches transforming the transformable line of maize called NP2222 (i.e. which has a normal A cytotype) with TALEN and CRISPR/Cas9 gene-editing machinery designed to target and knockout the maize PLA1/MATL gene located on chromosome 1, thereby resulting in a loss of function of MATL (¶0163). Que teaches the established lines that are homozygous for loss of function mutations in MATL are haploid inducer lines (¶0163). Que also teaches the NP2222-HI plants are homozygous wild-type for a color marker, and teaches in alternative embodiment the marker may be selected from a group including C1 (¶0157, 1066-0167).
However, Que does not disclose, teach, or otherwise render obvious wherein the maize plant is at least heterozygous for a wild-type allele at a color inhibitor locus in the maize plant that corresponds to a color inhibitor locus located on chromosome 9 between position 8 Mb and 10 Mb in the B73v5 reference genome. This is because the claim appears to be referencing Anthocyanin regulatory C1 protein-like (C1) which does not appear to be within the claimed positions of the B73v5 reference genome. A previous version that is the B73v4 reference genome comprises the C1 gene located at 8,983,450 - 8,984,644 on chromosome 9, which is within 8 Mb and 10Mb of chromosome 9. In the claimed B73v5 reference genome, however, C1 is located at 11,117,170 - 11,118,364 on chromosome 9 which is not within the claimed 8 Mb to 10Mb position (See maizegbd.org). For this reason, claim 12 appears free of the prior art.
Conclusion and Inquiries
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA N STOCKDALE whose telephone number is (703)756-5395. The examiner can normally be reached M-F 8:30-5:00 CT.
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JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662