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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 09/14/2026 has been entered.
Claim Status
Claims 1, 3-4, 10-12, 14-15, 17-18, 20, 22, 30-31, 33, 35-36, 38-39 and 44 are pending. Claims 1, 20, and 39 are currently amended. Claims 1, 3-4, 10-12, 14-15, 17-18, 20, 22, 30-31, 33, 35-36, 38-39 and 44 are examined on the merits.
Response to Amendment
The rejection of Claims 1, 3, 4, 12, 14, 17, 18, 20, 22, 35, 36, 38, 39, and 44 under 35 USC § 102(a)(1) under Anand is withdrawn in view of the amendments to claims. The claims are reconsidered below and are further rejected under 35 USC § 103, as set forth below.
The rejections of the claims previously rejected under 35 USC § 103 are maintained and modified in view of the amendments, as set forth below.
Claim Rejections - 35 USC § 103
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.
The claims are reconsidered below.
Claims 1, 3, 4, 12, 14, 15, 17, 18, 20, 22, 33, 35, 36, 38, 39, and 44 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (Ajith Anand et. al., US 20170121722A1, Application 2016-08-26, Publication 2017-05-04), in view of Hymus (Graham J. Hymus et. al., US10184130B2, Application of 2014-10-31, Publication of 2019-01-22).
Claim 1 (BRI): Under BRI consistent with the specification, claim 1 is drawn to a method of producing a regenerable plant structure comprising: introducing into maize plant cell a polynucleotide encoding a polypeptide that has at least 90% sequence identity across the entire length of any one of the recited reference polypeptides; and culturing the maize plant cell to produce the regenerable plant structure.
"introduced" means providing a nucleic acid (e.g., expression construct) or protein into a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell and includes reference to the transient provision of a nucleic acid or protein to the cell. “introduced” includes reference to stable or transient transformation methods. Thus, "introduced" in the context of inserting a nucleic acid fragment (e.g., a recombinant DNA construct/expression construct) into a cell, means "transfection" or "transformation" or "transduction" and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., nuclear chromosome, plasmid, plastid, chloroplast, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA) (paragraph 0022). Thus, claim 1 does not require any particular transformation method, promoter, or genomic integration. A “regenerable plant structure” reasonably includes callus, somatic embryos, shoots, or any plant tissue capable of regeneration.
Thus, claim 1 does not require any particular transformation method, promoter, or genomic integration. A “regenerable plant structure” reasonably includes callus, somatic embryos, shoots, or any plant tissue capable of regeneration.
Anand teaches transforming plant cells, including maize plant cells, by introducing an expression construct comprising a nucleotide sequence encoding a WUS/WOX homeobox polypeptide (claim 1; pa0013).
Anand further teaches allowing expression of the WUS/WOX polypeptide in each transformed cell to form a regenerable plant structure in the absence of exogenous cytokinin, wherein no callus is formed, and germinating the regenerable plant structure to form a transgenic plant (claim 1-3).
Anand does not expressly teach a polypeptide having at least 90% sequence identity across the entire length of one of the presently recited SEQ ID NOs.
Hymus teaches WUSCHEL/WUSCHEL-related homeobox (WOX) polypeptides and closely related sequences. Particularly, Hymus teaches SEQ ID NO: 318, identified as Si/Si004427m, as a WOX-related polypeptide comprising a conserved homeodomain (Column 67-68, Table 10). Amino acid sequence comparison shows that Hymus SEQ ID NO: 318 shares 99.1% sequence identity across the full-length comparison with instant SEQ ID NO: 3. Therefore, Hymus SEQ ID NO: 318 satisfies the limitation requiring a polypeptide having at least 90% sequence identity across the entire length of instant SEQ ID NO: 3.
It would have been obvious to one of ordinary skill in the art at the time of the invention to use the WOX-related polypeptide taught by Hymus in the WUS/WOX-based maize transformation and regeneration method of Anand because Anand teaches the use of WUS/WOX morphogenic regulators for maize transformation and regeneration, while Hymus teaches closely related WOX regulatory polypeptides for expression in plants. One of ordinary skill in the art would have had a reasonable expectation of success because Hymus SEQ ID NO: 318 is a closely related WOX polypeptide having a conserved homeodomain and shares 99.1% sequence identity across the full-length comparison with instant SEQ ID NO: 3.
Therefore, claim 1 is prima facie obvious over Anand in view of Hymus.
Claim 3 depends from claim 1 and recites the method, wherein the polynucleotide is operably linked to a heterologous promoter functional in a plant cell.
Anand teaches a recombinant expression cassette in which the introduced polynucleotide is operably linked to a promoter functional in a plant cell to express the encoded polypeptide (claim 7). Such a promoter in an introduced recombinant construct is a heterologous promoter (claim9).
Claim 4 depends from claim 1 and recites the method, wherein the polynucleotide is stably incorporated into the genome of the maize plant cell, or wherein the polynucleotide is transiently expressed in the maize plant cell.
Anand teaches stable transformation of plant cells, including maize plant cells, in which an introduced polynucleotide is incorporated into the genome (paragraph 0249). Anand also teaches transient expression of introduced polynucleotides in plant cell without genomic integration (paragraph 0208).
Claim 12 depends from claim 1 and recites the regenerable plant structure comprises a somatic embryo, embryogenic callus, somatic meristem, organocallus, a shoot, or a shoot further comprising roots.
Anand teaches culturing transformed maize cells to regenerated plants, which necessarily includes production of at least one regenerable plant structure selected from a shoot and/or a shoot comprising roots during regeneration (paragraph 0058).
Claim 14 is drawn to the method of claim 1, wherein expression of the polypeptide results in an increased somatic embryo induction frequency or increased embryo productivity relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
Anand teaches that expression of the disclosed polypeptide increases somatic embryo response/induction frequency across a population of infected immature cotyledons relative to a control (paragraph 0304 and fig 17A).
Claim 15 is drawn to the method of claim 14, wherein the somatic embryo induction frequency is increased at least about 50% - 95%, optionally wherein the somatic embryo induction frequency is increased at least 2, 5, 10, and 20-fold relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
For the same reason set forth above with respect to claim 14, Anand further teaches that expression of WUS2 increased somatic embryo production in maize. In Example 14, Anand reports that 84%, 69%, and 57% of immature embryos from maize inbreds PH184C, HC69, and PHH5G, respectively, produced somatic embryos following expression of WUS2 alone, and that 100%, 100%, and 91% respectively, produced somatic embryos following expression of WUS2 in combination with ODP2 (Table 12; pa0286-0287). Anand further teaches that WUS expression substantially improved somatic embryogenesis compared with a negative control lacking WUS expression (pa0303-0304).
Accordingly, Anand teaches increased somatic embryo induction frequency resulting from expression of the morphogenic regulator, including increases within the range recited in claim 15.
Claim 17 is drawn from claim 1 and further recites introducing a genome editing system in the maize plant cell.
Anand teaches that the disclosed methods and compositions are used to introduce into plants polynucleotides useful to target a specific site for modification in the genome, including by TALENs, meganuclease, zinc finger nucleases, and CRISPR-Cas, and discloses introducing a CRISPR-Cas system into plants for genome modification of a target sequence in a plant or plant cell (paragraph 0166).
Claim 18 is drawn to the method of claim 17, wherein the genome editing system comprises a CRISPR-based system, wherein the CRISPR-based system comprises (i) an RNA-guided nuclease or a polynucleotide encoding the RNA-guided nuclease; and (ii) a guide RNA or a polynucleotide encoding the gRNA under BRI.
Anand teaches a CRISPR/Cas genome editing system in which short RNA (crRNA and tracrRNA, or a single guide RNA) directs a Cas endonuclease to a DNA target to cleave the target (paragraph 0181, 0184, 0185).
Anand further teaches that a guide nucleotide/guide polynucleotide forms a complex with a Cas endonuclease and enables the Cas endonuclease to recognize and optionally cleave a DNA target site, including as a single guide molecule comprising targeting and Cas-recognition domains (paragraph 0182-0185).
Accordingly, claims 1, 3, 4, 12, 14, 15, 17, and 18 are prima facie obvious over Anand in view of Hymus for the reasons set forth above.
Claim 20 is drawn to a maize plant cell comprising a polynucleotide encoding a polypeptide having at least 90% - 99.5% sequence identity across the entire length of one of the listed polypeptides, wherein callus growth, somatic embryogenesis, and/or regeneration capacity of the maize plant cell is increased relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide under the same culture conditions.
Anand does not expressly teach a polypeptide having at least 90% sequence identity across the entire length of one of the presently recited SEQ ID NOs. However, Hymus teaches SEQ ID NO: 318, identified as Si/Si004427m, as a WOX-related polypeptide comprising a conserved homeodomain (Column 67-68, Table 10). Amino acid sequence comparison shows that Hymus SEQ ID NO: 318 shares 99.1% sequence identity across the full-length comparison with instant SEQ ID NO: 3. Thus, Hymus teaches the recited sequence-identity limitation for the same reasons set forth above for claim 1.
Anand further teaches that expression of WUS/WOX morphogenic regulators increases somatic embryo induction frequency relative to a control (paragraph 0304; fig 17A) and supports regeneration of transformed maize plants from transformed maize cells (paragraph 0245-0247; paragraph 0281), thereby disclosing increased somatic embryogenesis and/or regeneration capacity as recited in claim 20.
It would have been obvious to use the WOX-related polypeptide of Hymus in Anand’s maize plant cell for the same reasons set forth above for claim 1, with a reasonable expectation of success. Therefore, claim 20 is prima facie obvious over Anand in view of Hymus.
Claim 22 is drawn to the maize plant cell of claim 20, wherein the polynucleotide is operably linked to a heterologous promoter functional in a plant cell, which is the same promoter limitation recites in claim 3.
Claim 33 is drawn to the maize plant cell of claim 20, wherein the somatic embryo induction frequency is increased at least about 50% - 95%, optionally wherein the somatic embryo induction frequency is increased at least 2, 5, 10, and 20-fold relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
For the same reason set forth above with respect to claim 20 and 15, Anand teaches the additionally recited increase in somatic embryo induction frequency.
Claim 35 depends from claim 20 and further recites the maize plant cell comprising a genome editing system, which corresponds to the same genome-editing system limitation recited in claim 17.
Claim 36 is drawn to the maize plant cell of claim 35, wherein the genome editing system comprises a CRISPR-based system, wherein the CRISPR-based system comprises (i) an RNA-guided nuclease or a polynucleotide encoding the RNA-guided nuclease; and (ii) a guide RNA or a polynucleotide encoding the gRNA under BRI.
Claim 36 recites the same genome-editing system limitation as claim 18, but in the context of a maize plant cell.
Claim 38 recites a maize plant, tissue, organ, callus, or cell culture comprising the maize plant cell of claim 20.
Anand discloses producing transgenic T0 maize plants from Agrobacterium transformed maize immature embryos expressing WUS2 and ODP2, thereby providing a maize plant/tissue/cell culture comprising the transformed maize plant cell (e.g., somatic embryos and regenerated plants) (paragraph 0245-0247, and 0281).
Claim 44 is drawn to a method for producing a maize plant by regenerating a maize plant from the maize plant cell of any one of claim 20.
Anand further teaches regenerating a whole maize plant from the transformed maize plant cell (plant regeneration from the modified cell), thereby meeting the “regenerating a maize plant from the maize plant cell” limitation (example 1).
Therefore, Anand discloses the additional limitations of claims 22, 33, 35, 36, 38 and 44. Accordingly, claims 22, 35, 36, 38 and 44 are prima facie obvious over Anand in view of Hymus for the same reasons set forth above for claim 20.
Under the broadest reasonable interpretation, claim 39 is drawn to a recombinant polynucleotide expression construct comprising a polynucleotide encoding a recited morphogenic polypeptide (or a sequence-identity variant thereof) operably linked to a heterologous promoter functional in a plant cell.
As set forth above for claims 1 and 3, Anand discloses WOX-family morphogenic regulator coding sequences used for improving transformation efficiency in nucleic acid constructs that include a promoter for producing the nucleic acid in a plant cell.
Anand does not expressly teach the presently recited sequence-identity limitation. However, as set forth above for claim 1, Hymus teaches SEQ ID NO: 318, identified as Si/Si004427m, as a WOX-related polypeptide comprising a conserved homeodomain (Column 67-68, Table 10). Amino acid sequence comparison shows that Hymus SEQ ID NO: 318 shares 99.1% sequence identity across the full-length comparison with instant SEQ ID NO: 3.
It would have been obvious to use the WOX-related polypeptide of Hymus in Anand’s plant expression construct for the same reasons set forth above for claim 1, with a reasonable expectation of success.
Therefore, claim 39 is prima facie obvious over Anand in view of Hymus.
CURRENT FILING DATE: 2016-06-09
PRIOR APPLICATION NUMBER: PCT/US14/63345
PRIOR FILING DATE: 2014-10-31
PRIOR APPLICATION NUMBER: 61/900,224
PRIOR FILING DATE: 2013-11-05
NUMBER OF SEQ ID NOS: 546
SEQ ID NO 318
LENGTH: 343
TYPE: PRT
ORGANISM: Setaria italica
FEATURE:
OTHER INFORMATION: Si004427m
Query Match 99.1%; Score 1749; Length 343;
Best Local Similarity 96.5%;
Matches 331; Conservative 0; Mismatches 0; Indels 12; Gaps 1;
Qy 1 MEAAPQHGGAGVIDLEGSGSGGAPLSPPLSPASAAAAALANARWNPTKEQLAALEGLYEH 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEAAPQHGGAGVIDLEGSGSGGAPLSPPLSPASAAAAALANARWNPTKEQLAALEGLYEH 60
Qy 61 GLRTPSAEQIKQITARLREHGHIEGKNVFYWFQNHKARQRQKQKQDSFAYFTRLLRRPPP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GLRTPSAEQIKQITARLREHGHIEGKNVFYWFQNHKARQRQKQKQDSFAYFTRLLRRPPP 120
Qy 121 LPMLVRPPGPLPYPHGRLPVPAPPAAAAAACSSSNGGTH------------VMYRSPFYM 168
||||||||||||||||||||||||||||||||||||||| |||||||||
Db 121 LPMLVRPPGPLPYPHGRLPVPAPPAAAAAACSSSNGGTHVVEWINASFLAAVMYRSPFYM 180
Qy 169 PAAPQAPAANALYYHPQHQHQVPASVMYPRMEVAQDKMIPAAAQHNHHHHRHHPAAGAMY 228
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PAAPQAPAANALYYHPQHQHQVPASVMYPRMEVAQDKMIPAAAQHNHHHHRHHPAAGAMY 240
Qy 229 HAAAAGNNASTTPMHVLHFPPAAAVDAGPSRETLQLFPLQPTFLLPADKGRAAGGGASMA 288
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 HAAAAGNNASTTPMHVLHFPPAAAVDAGPSRETLQLFPLQPTFLLPADKGRAAGGGASMA 300
Qy 289 PAPSTASASFSGESESLEESPDSYSEALAVPFYDFFGLQSGGR 331
|||||||||||||||||||||||||||||||||||||||||||
Db 301 PAPSTASASFSGESESLEESPDSYSEALAVPFYDFFGLQSGGR 343
Claims 10 and 30 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (2017) and Hymus (2019) as applied claims 1 and 20, in view of Sun (Yuejin Sun et. al., WO2021030242A1, Application filed 2020-08-10, Published 2021-02-18).
Claims 1 and 20 as the teaching of Anand and Hymus is discussed above.
Claim 10 is interpreted as dependent of claim 1.
Claim 30 is interpreted as dependent of claim 20.
Claim 10 depends from claim 1 and further recites introducing a polynucleotide encoding a polypeptide having at least 90% - 99.5% sequence identity across the entire length of SEQ ID NO: 5 or 6 in the maize plant cell.
Anand and Hymus teach the method of claim 1 as set forth above, Anand does not expressly teach the additional polynucleotide encoding a polypeptide having at least 90% sequence identity across the entire length of instant SEQ ID NO: 5 or 6.
Sun teaches improving plant transformation efficiency by transforming plants (including maize) with morphogenic regulator constructs and further discloses embodiments comprising introducing a nucleic acid encoding a BABY BOOM (BBM) polypeptide (page 34, line 5-10), wherein Sun identifies BBM gene sequence including SEQ ID NO:179 (claim 17).
Based on an amino acid sequence alignment, the polypeptide encoded by instant application SEQ ID NO:6 shares 96.71% sequence identity with the polypeptide sequence of Sun’s WO2021030242A1 SEQ ID NO:179 across the entire length (below), which satisfies the limitation “at least 90% - 99.5% sequence identity” to SEQ ID NO:6 as recited in claim 10.
Therefore, Sun teaches introducing into a maize plant cell a polynucleotide encoding a BBM polypeptide meeting the claimed sequence identity requirement to SEQ ID NO:6, as additionally recited in claim 10.
It would have been obvious to one of ordinary skill in the art to include the additional BBM polynucleotide taught by Sun in the WUS/WOW-based maize transformation/regeneration method of Anand as modified by Hymus to improve regeneration and transformation efficiency, with a reasonable expectation of success.
Claim 10 is prima facie obvious over Anand, Hymus and Sun.
Claim 30 depends from claim 20 and further recites a polynucleotide encoding a polypeptide having at least 90% - 99.5% sequence identity across the entire length of SEQ ID NO: 5 or 6, which is the same additional “SEQ ID NO: 5 or 6” limitation recited in claim 10.
Anand and Hymus teach the maize plant cell of claim 20 as set forth above. Sun further teaches use of a BABY BOOM amino acid sequence together with a WOX morphogenic regulator to improve plant transformation/regeneration efficiency. It would have been obvious to include the additional BABY BOOM polynucleotide taught by Sun in Anand’s WUS/WOX-based maize plant cell as modified by Hymus to improve regeneration and transformation efficiency with a reasonable expectation of success.
Claim 30 is prima facie obvious over Anand in view of Hymus and Sun.
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Claims 11 and 31 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (2017) and Hymus (2019) as applied claim 1 and 20, in view of Lowe (Keith Lowe et. al., The Plant Cell (2016) Vol. 28: 1998–2015).
Claims 1 and 20 as the teaching of Anand and Hymus is discussed above.
Claim 11 is interpreted as depend of claim 1.
Claim 31 is interpreted as depend of claim 20.
Claim 11 is drawn to the method of claim 1, wherein the maize plant cell is of a germplasm having no somatic embryo induction when lacking the polynucleotide encoding the polypeptide under the same culture conditions.
Anand and Hymus teach the method of claim 1 as set forth above. Lowe further teaches maize inbred lines that are normally recalcitrant to hormone-mediated organogenesis or somatic embryogenesis from leave (p2010, “Discussion”). Lowe further teaches that, upon Agrobacterium-mediated delivery of Bbm/Wus2, the maize cells divide and appear to be the source of embryogenic, regenerable callus (p2010, “Discussion”).
Therefore, it would have been obvious to one of ordinary skill in the art at the time of the invention to apply the morphogenic regulator taught by Anand in view of Hymus to recalcitrant maize germplasm as taught by Lowe, with a reasonable expectation of improving somatic embryogenesis and regeneration.
Accordingly, claim 11 is prima facie obvious over Anand in view of Hymus and Lowe.
Claim 31 is drawn to the maize plant cell of claim 20, wherein the maize plant cell is of a germplasm having no somatic embryo induction when lacking the polynucleotide encoding the polypeptide under the same culture conditions.
Anand in view of Hymus teaches the maize plant cell of claim 20 as set forth above. Lowe teaches regeneration of recalcitrant maize germplasm using morphogenic regulators for the same reasons set forth above for claim 11.
Accordingly, claim 31 is prima facie obvious over Anand in view of Hymus and Lowe for the same reasons set forth above for claim 11.
Response to Applicant’s Remarks:
Applicant argues that Anand does not teach a polypeptide having the recited sequence identity to any of the sequences remaining in amended claims 1, 20, and 39, and that Sun and Lowe do not cure this deficiency.
Applicant’s arguments have been considered. The prior rejections are withdrawn. However, as discussed above, Hymus teaches SEQ ID NO: 318, which shares 99.1% sequence identity across the full-length comparison with instant SEQ ID NO: 3 and therefore meets the sequence identity limitation of amended claims 1, 20, and 39. Accordingly, the claims are rejected based on the combinations set forth above.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
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