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 8-12 and 17-45 are cancelled.
Claims 1-7 and 13-16 are pending.
Claims 1-7 and 13-16 are examined herein.
Upon further consideration, the limitations of previous claim 12 (now incorporated into claim 1) are no longer considered free of the prior art (see 103 rejection below).
Claims 1-7 and 13-16 are rejected.
Claim Interpretation
The qCYTO-A_TF3.1 QTL is interpreted to be on chromosome 3 between markers SM3158 at B73v5 position 14,742,407 and SM4586 at B73v5 position 70,562,070)
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.
Claim Objections
Claim 1 is objected to because of the following informalities: Claim 1 recites “wherein the selectable marker is homozygous for” which should read “wherein the plant is homozygous for the selectable marker of…”, or an equivalent that clarifies it is the plant that is homozygous for the selectable marker. Appropriate correction is required.
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 2, 4-7, and 14 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 2, 4-7, and 14 recite the limitation "The maize plant of claim , wherein”. The claims fail to depend from a preceding claim and therefore there is insufficient antecedent basis for the limitations in the claims.
For purposes of examination, claims 2 and 5 are interpreted to depend from claim 1, claim 4 is interpreted to depend from claim 3, claim 6 is interpreted to depend from claim 5, claim 7 is interpreted to pend from claim 6, and claim 14 is interpreted to depend from claim 13 (as is seen in the previous claim set dated 12/15/2025).
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 and 13-16 are rejected under 35 U.S.C. 103 as being unpatentable over Que (US-20190136250-A1), Chen (US-20180092316-A1), and Sarkar (Sarkar, K. R., & Coe Jr, E. H. (1966). A genetic analysis of the origin of maternal haploids in maize. Genetics, 54(2), 453.).
This is a modified rejection from the previous rejection set forth in the Office Action dated 03/10/2026.
Claim 1 is drawn to a maize plant homozygous for a loss-of-function mutation in the patatin-like phospholipase A2α gene (MATL) and at least heterozygous for a haploid inducer (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,
wherein the maize plant comprises a selectable marker,
wherein the selectable marker is homozygous for 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,
and 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.
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 qhir8).
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 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). 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). 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 least one quantitative trait locus (QTL) associated with increased haploid induction (HI-QTL); and 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 (remaining limitations 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 qhir8) (claim 3)
wherein the HI allele at the HI-QTL qhir8 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). In other analogous art, Sarkar teaches it is useful for one parent to be homozygous for the colored aleurone WT allele (C C) as opposed to the colour inhibitor allele (Ci Ci) that is carried by the other parent for identification of haploid embryos (p. 454, Materials and Methods).
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). Additionally, because the claim only requires 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, and further because the instant specification describes a color inhibitor locus at this location as a locus with either a WT allele that allows for color accumulation in embryos that results from R1-SCM2 allele (whereas the color inhibitor allele inhibits this pigment accumulation), the colored aleurone allele that produces kernels with colored-scutellum embryos (as opposed to color inhibitor allele) taught by Sarkar is reasonably interpreted to correspond to a color inhibitor locus located on chromosome 9 between position 8 Mb and 10 Mb in the B73v5 reference genome. It would be prima facie obvious to include a maize plant with the wild-type allele to assist in identification of haploid embryos, as taught by Sakar, and also to prevent of color inhibition (caused by color inhibitor allele) of the color that is imparted by a marker gene in the embryo including, e.g,. R1-SCM2.
Claims 5-7 are rejected under 35 U.S.C. 103 as being unpatentable over Que, Chen, and Sarkar 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 transformation (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, Chen, and Sarkar teach the limitations of claim 1 as set forth in the previous obviousness rejection. The teachings of Que, Chen, and Sarkar as they are applied to claim 1 are set forth previously herein and are incorporated by reference.
However, Que, Chen, and Sarkar 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).
Response to Arguments
Applicant argues beginning on p. 1 of remarks dated 06/02/2026 the
following arguments:
Claim 1 is objected to for the recitation of the “HI” abbreviation. Herein, claim 1 is amended recite “haploid inducer (HI)”. Applicant believes the amendment overcomes the objection and requests withdrawal.
Similarly, claims 5 and 17 are objected to for the recitation of the “TF” abbreviation. As amended herein, claim 17 is cancelled and claim 5 now recites “transformation (TF) allele”. Applicant believes the amendments overcome the objection and requests withdrawal.
Claim 12 is objected to for being dependent on a rejected base claim. The Examiner states if claim 12 is rewritten as an independent claim including limitation of the base claim and intervening claims, it would be allowable. Solely to advance prosecution and not to acquiesce the Examiners rejections, Applicant has amended claim 1 to incorporate claim 12 and intervening claims accordingly. Applicant submits these amendments overcome the objection.
No new matter has been added by way of these amendments.
Examiner’s Response:
In view of Applicant’s amendments, the objections have been withdrawn.
Upon further consideration, the limitations of previous claim 12 (now incorporated into claim 1) are now rejected under 35 USC 103 (see rejection above).
Applicant argues beginning on p. 1 of remarks dated 06/02/2026 the
following arguments:
Claims 7, 9-12, and 19 are rejected for allegedly being indefinite in the recitation of qCYTO-A_TF3.1. Claims 9-12 have been incorporated into claim 1. Claim 19 is cancelled. Applicant respectfully disagrees with the indefiniteness rejection because paragraphs [0164] – [0165] of the specification detail the location of the qCYTO-A_TF3.1 QTL. Paragraph [0164] states that the QTL identified on chromosome 3 is located between markers SM3158 (position 14, 7442,407) and SM4586 (position 70,562,070). Therefore, the disclosure defines the QTL by its precise genomic coordinates on the well-known B73v5 genome. It goes on to say the other markers (SM4787, SM3814, SM3362, and SM0634AQ) are all positioned between SM3158 and SM4586 and states they may also work to identify the QTL. With that description, as well as the statement “Based on this information, selection for plants having the SYN-INBC34 allele at this QTL (referred to herein as qCYTO-A_TF3.1…)” in paragraph [0165], one of ordinary skill in the art would understand the definition of qCYTO-A_TF3.1 (the QTL on chromosome 3 between markers SM3158 and SM4586 defined by genomic position).
Additionally, the Examiner states it is unclear which markers are required according to Table 6 because Table 21 identifies lines with varying presence of the markers from Table 6. Applicant respectfully disagrees. Table 6 provides the appropriate primers and probes for both the SM3158 and SM4586 markers. Paragraph [0096] of the specification states, “the assay to identify the TF allele at the qCYTO-A_TF3.1 TF-QTL comprise genotyping an individual at one or more of the markers SM3158, SM4787, SM3814, SM3362, SM0634A, and SM4586” (emphasis added). Again, as stated in the specification, the QTL on chromosome 3 is between markers SM3158 and SM4586.
Claim 9, and dependent claims 10-12, is rejected for allegedly being indefinite in its recitation of “a selectable marker”. As amended herein, claim 9 (as well as 10-12) is cancelled, rendering the rejection moot.
Examiner’s Response:
The previous rejections under 35 USC 112(b) to claims 7, 9-12, and 19 are withdrawn in view of Applicant’s amendments and arguments. The qCYTO-A_TF3.1 QTL is interpreted to be on chromosome 3 between markers SM3158 at B73v5 position 14,742,407 and SM4586 at B73v5 position 70,562,070) as described in Applicant’s argument above and the specification (¶0164).
However, new rejections under 35 USC 112(b) have been made in view of Applicant’s amendments (see 112(b) rejection above).
Applicant argues beginning on p. 2 of remarks dated 06/02/2026 the
following arguments:
Claims 17 and 20 are rejected for allegedly being anticipated by Lowe and Allen. Applicant respectfully disagrees. However, solely to advance prosecution, and not to acquiesce the Examiner’s rejection, Applicant submits that claims 17-20 are cancelled herein and requests withdrawal of the rejection.
Examiner’s Response:
In view of Applicant’s cancellation of the claims, the rejections under 35 USC 102 have been withdrawn.
Applicant argues beginning on p. 2 of remarks dated 06/02/2026 the
following arguments:
Claims 1-4, 8-10, and 13-16 are rejected for allegedly being obvious over Que and Chen. Applicant respectfully disagrees. However, solely to advance prosecution and not to acquiesce the Examiner’s rejection, the claims are amended herein so that subject matter of claims 8-12 are incorporated into claim 1 based on page 3 of the Action where the Examiner states claim 12 would be allowable if rewritten in independent form to include the base claim and intervening claims. With the present amendments, Applicant submits the claims are non-obvious over Que and Chen and requests withdrawal of the rejection.
Claims 5-7 are rejected for allegedly being obvious over Que and Chen and further in view of Lowe and Salvo. Applicant submits claims 8-12 are incorporated into claim 1 as suggested by the Examiner on page 3 of the office action, overcoming the rejections. The amended claims submitted herewith are non-obvious. Applicant requests withdrawal.
Claim 11 is rejected as allegedly being obvious over Que and Chen and further in view of Chintamanani. Applicant submits claims 8-12 are incorporated into claim 1 as suggested by the Examiner on page 3 of the office action, overcoming the rejections. The amended claims submitted herewith are non-obvious. Applicant requests withdrawal.
Claims 18-19 are rejected for allegedly being obvious over Lowe and further in view of Salvo. Solely to advance prosecution, claims 18 and 19 are cancelled.
Examiner’s Response:
Upon further consideration, the limitations of previous claim 12 (now incorporated into claim 1) are no longer considered free of the prior art in view of Sarkar (see 103 rejection above). For this reason, the claims remain rejected under 35 USC 103.
Conclusion
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
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