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 .
Election/Restrictions
The previous species election requirement is withdrawn in view of Applicant’s amendments to the claims.
Claim Status
Claims 1, 3-9 & 11-13 are under examination on the merits.
Claims 2 & 10 are canceled.
Priority
Foreign priority is claimed to ITALY 102022000010913.
Claims 1, 3-9 & 11-13 receive the U.S. effective filing date of 25 May 2022.
Claim Objections
Claim 1 is objected to because of the following informalities:
Grammatical/typographical error; lines 2-3 reads, “…both target genes selected from Glyma.19g119300 and Glyma.03g006600…”. Because the claim requires both genes the phrase ‘selected from’ adds nothing to the claim and potentially confuses whether one gene would satisfy the limitations. This would more properly read, “…both target genes ”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 3-8 & 13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The normal understanding of drought resistance is plants with drought resistance will perform better than the same plant without the drought resistance characteristic. In the best case, Applicant has shown a connection in stomatal control. There is no evidence that altering the stomatal control of soybean would lead to a more drought resistant plant. Additionally, the genes in question are MYB transcription factors which are linked to many other important soybean characteristics and can be pleiotropic. It is not clear if altering the stomatal control of a soybean plant would result in better performance under drought conditions as we don’t know how inactivating these two genes would impact other traits of responses regulated by these MYB60 like genes.
Claim 1, from which all others depend, recites a method of increasing drought resistance in soybean via targeted inactivation of two MYB genes, Glyma.19g119300 & Glma.03g006600. The claim requires a method which increases drought resistance in soybeans.
Review of the specification indicates Applicant has only made directed gene edits / knockouts of Glyma.19g119300 & Glyma.03g006600 in transgenic plants [Specification, p.11, l.16 ‘Editing of Soybean Genes’, p.18, l.16 ‘Soybean Transformation’]. Applicant does not describe whether the resulting plants have improved drought tolerance compared to un-modified controls. Examples of gene-edited lines and their evaluation for drought tolerance are described in future-tense, as-yet-performed (i.e. prophetic) examples [see p.21, l.4—p.25, l.4]. Applicant has not tested or measured the effects of their method on the stomatal response or drought tolerance of their soybean plants.
Drought resistance is a complex trait, conditioned by numerous genes and interactive biochemical signaling pathways, many of which interact with and are regulated by environmental variables [see p.6, Figure 2 in Li et al. Front. Genet. 13:1060529; Published 29 Nov 2022]. Modern technology makes it relatively routine to identify and modify a DNA sequence associated with one of these numerous genes. However, the directed modification of any one gene, or few genes, involved in such complex phenotypic traits requires validation to demonstrate the modifications truly result in the desired phenotype [see p.66, col.1, ¶.3-4 in Freitas-Alves et al. Journal of Advanced Research 73 (2025) 53–72; Published 18 Aug 2024].
One can clearly point to a mutation or genetic modification made in a DNA sequence, but absent demonstration of what the functional outcome of making that modification is, through presenting phenotypic data, the potential outcome of said modification is merely speculative.
Applicant clearly shows they have made modifications to the genome and edited two genes concurrently. They have not taken the resulting plants to the field and reported what the actual impact of those modifications (i.e. the claimed method) are with respect to drought tolerance. The described gene edits may or may not be a method of increasing drought resistance. Absent phenotypic/validation data, the disclosure is inconclusive.
Because Applicant has not described increased drought resistance, the written description does not reasonably convey to one skilled in the relevant art that the inventor had possession of the claimed invention. As such, claim 1 and its dependents are rejected.
Applicant is advised to cancel language drawn to drought resistance and focus claims on stomatal control.
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, 3-9 & 11-13 are rejected under 35 U.S.C. 103 as being unpatentable over Baldoni [Int. J. Mol. Sci. 2015, 16, 15811-15851; Published 13 Jul 2015] in view of Cominelli [Current Biology, Vol. 15, 1196–1200 (2005); Published 12 Jul 2005], Galbiati [BMC Plant Biology 2011, 11:142; Published 21 Oct 2011], and Chen [Plant Biotechnology Journal (2021) 19, pp. 702–716; Published 18 Oct 2020].
Baldoni teaches the role of MYB factors in drought response of plants [p.15812, ¶.2-3; p.15815, ¶.2-3; p.15813, Table 1]. They teach that directed manipulation or genetic engineering of MYB factors, including disruption of function (i.e. silencing), can produce plants with increased drought resistance [p.15839, ¶.3]. They teach AtMYB60 mutation impacts stomatal closure and drought tolerance, and that similar physiological function has been identified via AtMYB60 orthologs in other crops (i.e. grape, VvMYB60) [p.15819, ¶.3—p.15820, ¶.2 & p.15813, Table 1].
Baldoni does not teach the AtMYB60 soybean orthologs Glyma.19g119300 & Glma.03g006600 per se. Baldoni does not teach the inactivation of MYB genes via gene editing or use of CRISPR/Cas-9 systems and/or the necessarily associated sgRNAs.
Cominelli teaches that specific mutation of AtMYB60 induces stomatal closure, and that mutant Arabidopsis plants have increased resistance to drought [p.1197, col.1, ¶.2—p.1198, col.1, ¶.1]. They state directly to the reader that identification and modulation of such a stomata-specific transcription factor opens up new possibilities to improve drought resistance [p.1199, col.1, ¶.1].
Galbiati teaches the identification of AtMYB60 orthologs in other crop species and their conserved function in regulating stomata [p.2, col.1, ¶.4—p.4, col.1, ¶.1; p.3, Figure 1]. They teach that one can use the protein sequence of AtMYB60, and specifically the use of disclosed sequence motifs identifying of the specific MYB family to which AtMYB60 belongs [p.2, col.1, ¶.4]. Galbiati teaches that identification of multiple homologs via sequence comparison (i.e. BLAST search) can then be narrowed by comparison of distinct structural features of AtMYB60 orthologs. This includes identification of conserved R2R3 binding domains and exon/intron organization, a PHEEG signature encompassing glutamic acid residues connecting the R2R3 repeats, and presence/absence of distinct C-terminal repeat patterns distinguishing AtMYB60 from other related MYB sequences [p.2, col.2, ¶.2—p.4, col.1, ¶.1; p.3, Figure 1]. They teach that this method of identification of AtMYB60 orthologs in another crop species predictably points to a target or targets for engineering of stomatal response and potentially improving drought tolerance [p.9, col.1, ¶.1-col.2, ¶.1; p.11, col.1, ¶.1].
Chen teaches the identification of a drought-associated MYB ortholog in soybean and its mutation or knock-out using gene editing [p.713, col.1, ¶.3; p.711, col.2, ¶.2]. They teach the construction of an expression vector expressing Cas9 under control of the CaMV35S promoter, sgRNAs corresponding to the target ortholog and driven by the species-specific corresponding promoter, and transformation of soybean via Agrobacterium [p.713, col.1, ¶.3]. They teach the testing & validation of resulting gene-edited mutations via drought stress trials [p.712, col.2, ¶.2—p.713, col.1, ¶.1].
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to arrive at a method of using a MYB transcription factor to improve drought resistance in a crop plant, as taught by Baldoni, which relied on disruption of stomatal function involving AtMYB60 genes outlined by Cominelli, to one targeting sequence-identified AtMYB60 orthologs in other plant species and whose knock-out prevents stomatal opening (i.e. increases drought tolerance) as taught by Galbiati. It would be obvious to generate such engineered mutations with the most current tools of molecular biology, such as gene-editing systems clearly laid out in soybean and known to work in targeting MYB genes as reported by Chen.
One of ordinary skill in the art would have been motivated to combine these teachings to obtain the described benefit of reduced stomatal opening, and presumably improved drought tolerance, in a soybean plant. Approaches to such directed manipulation of stomata function via AtMYB60 orthologs in other crops such as grape was described by Galbiati. Use of gene-editing to manipulate MYB genes involved in drought in soybean, specifically, was known to be an effective way to cross-apply engineering or manipulation of already known AtMYB orthologs, outlined by Chen.
One skilled in the art would be motivated to apply the known MYB gene-editing method Chen describes in soybean to the orthologous AtMYB60 targets which were well-known to be involved in stomata function and drought response in order to create a plant which is more productive during drought conditions, as first suggested by Cominelli.
Regarding claims 1 & 9; these are drawn to generation of a drought-resistant soybean plant via inactivation of Glyma.19g119300 & Glyma.03g006600, which appear to be orthologs of AtMYB60 [Specification, p.7, l.19—p.8, l.4]. Baldoni describes the function of MYB genes in condition drought tolerance and Cominelli specifically describes AtMYB60 as a target to generate drought resistant crops [p.15812, ¶.2-3; p.15815, ¶.2-3; p.15813, Table 1; p.15812, ¶.2-3; p.15815, ¶.2-3; p.15813, Table 1]. Galbiati describes the process of using known sequence to find AtMYB60 orthologs in other crops [p.2, col.1, ¶.4—p.4, col.1, ¶.1; p.3, Figure 1].
Regarding claims 3-8 & 11-13; these are drawn to use of CRISPR/Cas-9 gene editing to knock out or disrupt function of the target MYB genes Glyma.19g119300 & Glyma.03g006600. Chen describes the use of gene editing to engineer drought-associated MYB genes in soybean, including use of CRISPR/Cas-9 to disrupt MYB genes [p.713, col.1, ¶.3; p.711, col.2, ¶.2].
With respect to particular guide sequences of SEQ ID NO.1-60 to be used for gene-editing (i.e. claims 4 & 5), crop-specific promoters (i.e. claim 7), and optimal tissues to use for transformation and/or tissue culture (i.e. claim 13); such design elements are routine in their optimization, as he development of appropriate gene-editing and/or transformation constructs from soybean genomic sequence data and the known AtMYB60 is taught in both Chen and in Galbiati [p.713, col.1, ¶.3; p.711, col.2, ¶.2; p.2, col.1, ¶.4—p.4, col.1, ¶.1; p.3, Figure 1].
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 EST.
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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
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