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
Amendment entered on 10/21/2025 is acknowledged. Claims 1-4, and 6-16 are pending and claims 15 and 16 are added by applicant as new claims. Since new claims 15 and 16 does not add further search burden the claims are examined in this office action.
Therefore, claims 1-4 and 6-16 along with the elected species of SEQ ID NO:90 as the spacer sequence from claim 12 and SEQ ID NO:83 as the region of amino acid sequence from claim 14 are examined in this office action.
Rejection that are withdrawn
Objection to specification is withdrawn in light of applicant’s amendment of specification to include a symbol ® after the terms used as are trade names or trade marks used in commerce.
Objections to claims are withdrawn in light of applicant’s amendment of claims 7 and 11 to include comma after recitation of “claim1” and by including describing the short forms in claim 8.
Rejection of claims over 35 U.S.C. 112(b) is withdrawn in light of applicant’s amendment of claim 10 to delete the parenthesis and claim 14 to recite “the promoter region”.
Claim Rejections - 35 USC § 112 -Written Description Requirement
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 1-4 and 6-16 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 claim(s) contains 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.
Following analysis is modified to analyze newly added claims 15 and 16.
Analysis of Breadth of Claims
Claims 1 and 16 recite large variants of SGR1 gene comprising any of the nucleotide’s sequence having at least 90% sequence identity to SEQ ID NOs: 75 and 77 and SGR2 gene comprising any of the nucleotide’s sequence having at least 90% sequence identity to SEQ ID NOs: 76 and 78.
Claim 12 recites large variants of spacer sequence having at least 90% sequence identity to SEQ ID NO: 90.
Claims 14 and 15 recites large variants of nucleotide sequence having at least 90% sequence identity to SEQ ID NOs: 81-82.
Claim 14 recites large variants of amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83.
Claim 1 recite any mutation (i.e. any substitution, an insertion and/or a deletion) generated in the promoter region of endogenous SGR1 gene and the SGR2 gene with target site of any structures.
Claim 1 recite any target site in the promoter region that would have any structure.
Any of the target site mutation would require to have increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant (claim 2).
What is Described in the Specification
Applicant describes:
SGR1 and SGR2 which are endogenous soybean genes (page 39, lines 22-23).
Specification describes SEQ ID NOs: 115-144 are example of edited endogenous SGR nucleic acid sequences as shown in Table 1 (page 7, lines 19-20) (see table below). Table 1 shows the deletion of different sizes for the wild type SGR1 identified as Locus 28 and SGR2 identified as locus 27.
Applicant describes promoter editing to generate knockdown of SGR1 and SGR2 (Page 73, lines 24-25).
To generate range of promoter alleles with multiple spacer sequences were designed across the promoters of SGR1 and SGR2 and placed into one construct (page 73, lines 28-30).
Vectors encoding the spacer as well as a CRISPR-Cas effector were introduced into soy using Agrobacterium (Table 2) (page 73, lines 32-33).
Molecular screening was employed to identify E0 plants carrying deletions in the promoters of both SGR1 and SGR2 (page 74, lines 1-4)
A dark induced leaf senescence assay was used to identify E1 plants that showed chlorophyll leaf senescence assay was used to identify E1 plants that showed chlorophyll expression (Fig. 4, Table 3) (page 74, lines 5-9).
Expression level of SGR 1/2 was assayed in a subset of lines that showed a range of phenotypes and edit types (Fig. 5) (page 74, lines 9-10).
Lines with SGR1/2 knockdown and minimal senescence delays and chlorophyll retention were selfed to get E2 seeds. Homozygous E2 lines were then subjected to greenhouse screening with a panel of isolates as well as field screening.
Two E1 lines that were homozygous for large deletions in SGR2 but heterozygous for large deletions in SGR1 were grown another generation to isolate homozygous edited lines (Table 3) that contain large deletions in both promoters (page 75, lines 9-12).
Difference Between What was described and What is Claimed
Applicant has not described variants of SGR1 gene comprising any of the nucleotide sequences having at least 90% sequence identity to SEQ ID NOs: 75 and 77 and SGR2 gene comprising any of the nucleotide sequences having at least 90% sequence identity to SEQ ID NOs: 76 and 78 (claims 1 and 16).
Applicant has not described variants of spacer sequence having at least 90% sequence identity to SEQ ID NO: 90 (claim 12).
Applicant has not described variants of nucleotide sequences having at least 90% sequence identity to SEQ ID NOs: 79-82 (claims 14 and 15).
Applicant has not described variants of amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83 (claim 14).
Applicant has not described any mutation (i.e. any substitution, an insertion and/or a deletion) generated in the promoter region of endogenous SGR1 gene and the SGR2 gene with target site of any structures would be useful.
Applicant has not described the target site in the promoter region which would have any structure (claim 1).
Applicant has not described any target site mutation would cause increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant (claim 2).
Applicant has not described any intended use of method of mutation and mutant plant with mutation in any portion of promoter region of the STAYGREEN (SGR) genes SGR1 and SGR2 in claims 1 and 3-13.
Analysis
The purpose of the written description is to ensure that the inventor had possession at the time the invention was made, of the specific subject claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
Applicant has not described large variants of SGR1 gene comprising any of the nucleotide sequences having at least 90% sequence identity to SEQ ID NOs: 75 and 77 and SGR2 gene comprising any of the nucleotide sequences having at least 90% sequence identity to SEQ ID NOs: 76 and 78. For example SEQ ID NO: 75 is 2298 nucleotide long. A variant of SEQ ID NO: 75 having at least 90% identity would have ~230 nucleic acid (NA) changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 75, and this encompasses a genus of nucleic acid sequence that includes at least ~4230 different molecules. For this reason, the genus of nucleic acid molecules having at least 90% identity to SEQ ID NO: 75 is an very large genus of molecules. Furthermore, applicant has not described large variants of nucleotides sequence having at least 90% sequence identity to SEQ ID NOs: 75-78. Similarly, Applicant has not described variants of coding sequences (cDNAs) as nucleotide sequence having at least 90% sequence identity to SEQ ID NOs: 81-82 of SGR1 and SGR2 (claim 14). Furthermore, Applicant has not described variants of nucleotide sequence having at least 90% sequence identity to SEQ ID NOs: 79-80 as mRNA sequences of SGR1 and SGR2 respectively as described in Spec, page 7, lines 11-12 (as claimed in claim 14).
It is known in the art that the SGR protein require specific motifs to be functional for specific traits. Jiao et al. (Published: 2020, Journal: Botanical studies, 61(1), 1-9); teaches stay green gene (SGR) homologs are widespread in the plant kingdom and the SGR proteins has specific conserved motifs (page 2, left last paragraph, Page 3, Figure 1). Jiao et al. teaches SGR homologs function in Chl degradation in leaf, seeds (page 6, right paragraph 2), alters expression of ethylene induced genes, ethylene receptor genes, ethylene signaling, carotenoid accumulation (page 6, right paragraph 3), nodule development (page 6, right paragraph 4). Jiao et al. teaches their phylogenetic analysis revealed that specific conserved SGR domain, chloroplast transit peptide, and variable C-terminal region are present in different SGR genes (page2, left last paragraph, see Figures 1-2). Therefore, applicant has not described at least 90% sequence identity to SEQ ID NOs: 75, 76 and 81-82 that would retain such conserved domains or motifs to have uses as a SGR gene to be modified for use as exhibit increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant as described in claim 12 and showed in specification.
Claim 12 recites variants of spacer sequence having at least 90% sequence identity to SEQ ID NO: 90. The SEQ ID NO: 90 is 23 nucleotide long. A variant of SEQ ID NO: 90 having at least 90% identity would have ~2 nucleic acid (NA) changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 90 anywhere in the sequence in any combination. Applicant has not described any spacer sequence having at least 90% sequence identity to SEQ ID NO: 90 would have been found useful for creating mutant SGR1 and SGR2 genes that would exhibit increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant other than SEQ ID NO:90 itself.
Applicant has not described variants of amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83 (claim 14). SEQ ID NO: 83 is 141 amino acid long. A variant of SEQ ID NO: 83 having at least 90% identity would have ~14 amino acids (AA) changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 83, and this encompasses a genus of nucleic acid sequence that includes at least ~2014 different molecules. Applicant has not described SGR gene encoding protein having a region comprising amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83.
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Furthermore, the state of the art at the time of the instant invention was that although the skilled artisan would appreciate the nucleic acid comprising SEQ ID NO: 75-82, and 90 and amino acid sequence of SEQ ID NOs: 83 one would not be able to readily predict function of nucleic acid which has at least 90% identity to SEQ ID NOs: 75-82, and 90 and amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83 and it is impossible to predict such a broad sequence variation will have any required function. For example, Guo et al. (Published Year: 2004, Journal: Proceedings of the National Academy of Sciences, Vol. 101(25), pages: 9205-9210) teaches that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (page 9209, right. col., paragraph 2).
Furthermore, it is known in the art that a variation in promoter region would affect the relative expression of endogenous genes. Rodríguez-Leal et al. (Published:2017, Journal: Cell 171:470–480) teaches deletion of different sizes of conserved region (i.e. CR1, CR2 etc.) in SlCLV3 promoter in different species of tomato (page 475, Figure 4E) provides continuum of locule number variation where relative expression of SICLV3 is reduced in for example in m6 and m3 where there is no changes in m12 and m8 (page 475, Figure 4F). Therefore, targeting different regions of the nucleotides would lead to various results in the expression of the genes leading to variation in the phenotypes.
Applicant has not described wherein any deletion in the promoter of SGR1 or SGR2 significantly increases disease resistance for example Figure 7 left pane shows CE35915 is not different than non-transformed control, furthermore CE35914, CE35906, CE40104, CE39930 also are no different than the non-transformed control (as shown with same mean comparison letters A and B). Thus if the percent severity similar in these edit call for each edited plant as compared to non-transformed control is observed in other mutation it is not predictable for example for CE35915 has edits on SGR1 and SGR2 sequences ranging from 5D to 70D and 6 insertions (I) (page 77, Table 3) which has mean disease rating not different from the untransformed control, in fact the rating is higher than the control (Figure 7) showing more disease even with the homozygous deletion lines having mutation in promoter regions of SGR1 and SGR2 sequences (Table 3, Figure 7).
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Same lower SPAD chlorophyll reading also seen in CE35915 as compared to control in all the DPI (9, 11, and 14) (see Figure 6), and chlorophyll retention as shown by proportion of green remaining pixels shown in Figure 4 also show CE35915, and CE5842 has pixel proportion same as control (Figure 4).
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Thus, it is not clear whether any mutation in promoter region of the SGR1 and SGR2 would have exhibited increase in resistance to soybean rust, delayed senescence and chlorophyll retention as compared to a control plant or part thereof not comprising the mutation.
Applicant does not describe the function of mutation to any portion of promoter region of STAYGREEN (SGR) genes SGR1 and SGR2 is predictable to have use for example edit type CE35915 for SEQ ID NOs: 130-133 (Spec, page 76, Table 1) shows no significant effect to any traits in soybean compared to non-transformed control (Drawing, Figure 7 and its mean comparison, Figure 4 and Figure 6).
Given the virtually large structural variable associated with these embodiments of any mutation in the promoter region of large variants of SGR gene and sequences with at least 90% identity, the claims read on an extremely broad and highly diverse structures that needs to have specific function to exhibit an increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control plant or part thereof not comprising the mutation. However, applicant has not reduced to practice any embodiments where a mutation in any portion of promoter region of the variants of the SGR1 and SGR2 can be effective to increase in resistance to soybean rust, delayed senescence and chlorophyll retention as compared to a control plant or part thereof without targeting specific regions of SGR1 and SGR2 genes. Thus, there is dearth of description any mutation in promoter regions of SGR1 and SGR2 that would have any uses or would be effective to increase resistance to soybean rust, causes delayed senescence and/or chlorophyll retention.
Given the large structural diversity associated with the claimed genus, Applicant’s disclosure is not representative of the claimed genus as a whole. This point is particularly relevant because, as discussed above, the prior art speaks to the disconnection between the structure of the broadly claimed variants of SGR1 and SGR2 genes in Soybean plants with no known function or with function of increased resistance to soybean rust, and that they cause delayed senescence and/or chlorophyll retention.
"The test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to one skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad Pharm, Inc, v EH Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Lockwood v. Amer. Airlines, ina, 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). "An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations. Lockwood, 107 F.3d at 1572, 41 USPG2d at 1966". While the written description requirement does not demand either examples or an actual reduction, actual "possession" or reduction to practice outside of the specification is not enough. Ariad Pharm, Inc. v. Eli Lilly & Co., 598 F,3d 1336,1352 (Fed. Cir. 2010). Rather, it is the specification itself that must demonstrate possession. Id.
The Federal Circuit has clarified the application of the written description requirement to inventions in the field of biotechnology. The court stated that, “A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or of a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus.” See University of California v. Eli Lilly and Co., 119 F. 3d 1559; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997).
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. As a result, it is not clear that Applicant was in possession of the claimed genus at the time this application was filed.
Response to Argument
Applicant's arguments filed 10/21/2025 have been fully considered but they are not persuasive.
Applicant argues claim 5 is canceled herein without prejudice or disclaimer, thereby mooting the rejection as applied to this claim (Response to Rejection, page 7, paragraph 4).
Applicant respectfully submits that the specification guides one skilled in the art to target a site in the promoter region of an endogenous SGR1 gene and a site in the promoter region of an SGR2 gene for mutation to provide a plant exhibiting an increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention. See at least FIGS. 2-3 and Example 1 of the specification. Applicant argues , the specification provides the nucleotide sequence of the promoter and genomic transcript of SGR1 and SGR2 (SEQ ID NOs:75-78), coding sequence of SGR1 and SGR2 (SEQ ID NOs:81-82), mRNA sequences of SGR1 and SGR2 (SEQ ID NOs:79-80), as well as the amino acid sequence of SGR1 and SGR2 (SEQ ID NOs:73-74) from soybean, and describes nucleotide sequences having 90% sequence identity to the SGR1 and SGR2 genes as including, e.g., homologs, that may be identified by methods such as computer-based alignments and hybridization under stringent conditions. See at least pages 20-24 of the specification (Response to Rejection, page 7, last paragraph).
Regarding argument about teaching of homologs, although one skilled in art would find homologs of recited sequences and Jiao et al. teaches such homologs and conserved motifs the argument were not found persuasive since there is no predictability that mutating any of those homologs would lead to changes in any useful functions or function of increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant. Furthermore, applicant has not described targeting which of the motifs or conserved region would lead to the change in which function of the protein. Therefore, there is dearth of description of method of mutating any nucleotide sequences having 90% sequence identity to the SGR1 and SGR2 genes would have change in any useful function other than the method mutating recited genes of SEQ ID NOs: 75-78 for function of increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention. Furthermore, regarding argument on skilled in the art would recognize the members of genus of sequences claimed, the argument was not found persuasive since applicant has not describes that the members of genus of sequences that when mutated would have useful function or would increase resistance to soybean rust, delayed senescence and/or chlorophyll retention. Applicant is claiming mutating large number of sequences any region of their promoters Instead applicant’s example only showed mutating at specific region of the promoter would cause increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention by modifying genes of SEQ ID NOs: 75-78.
For example, Figure 7 left pane shows CE35915 is not different than non-transformed control, furthermore CE35914, CE35906, CE40104, CE39930 also are no different than the non-transformed control (as shown with same mean comparison letters A and B). Thus if the percent severity similar in these edit call for each edited plant as compared to non-transformed control is observed in other mutation it is not predictable for example for CE35915 has edits on SGR1 and SGR2 sequences ranging from 5D to 70D and 6 insertions (I) (page 77, Table 3) which has mean disease rating not different from the untransformed control, in fact the rating is higher than the control (Figure 7) showing more disease even with the homozygous deletion lines having mutation in promoter regions of SGR1 and SGR2 sequences (Table 3, Figure 7).
Applicant argues in addition, the examples provide evidence that targeting the promoter region of the SGR1 and SGR2 genes for mutation is effective in producing soybean plants with reduced SGR1 and SGR2 expression, reduced senescence, chlorophyll retention, and increased resistance to soybean rust. See at least FIGS. 4-8. Applicant submits that the specification makes it clear that a soybean plant having a mutation in the promoter region of the SGR1 and SGR2 gene as claimed herein shows an increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control, thereby providing sufficient guidance to the skilled person to target the claimed region with the expectation that the soybean plant would exhibit an increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention (Response to Rejection, page 8, first paragraph).
Applicant argues at page 9 of the Office Action, it is asserted that Jiao et al. (Botanical Studies 61(1): 1- 9, 2020) teach that "stay green gene (SGR) homologs are widespread in the plant kingdom and the SGR proteins has specific conserved motifs." Applicant argues in addition, the Office Action suggests that Jiao et al. teach phylogenetic analysis, which "revealed that specific conserved SGR domain, chloroplast transit peptide, and variable C-terminal region are present in different SGR genes." See Office Action, page 9. Applicant assert that "applicant has not described at least 90% sequence identity to SEQ ID NOs: 75, 76 and 81-82 that would retain such conserved domains or motifs to have uses as a SGR gene to be modified for use as exhibit increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant" (See Office Action, page 9). Applicant submits that Jiao et al. show that one of ordinary skill in the art would have been well aware of the SGR genes in plants, including homologs, and the protein motifs encoded by the same. Applicant argues in this context, using the sequences and guidance disclosed in the specification, one of skill in the art could readily 'visualize or recognize' the members of the genus of sequences claimed. Ariad, 598 F.3d at 1350 (Response to Rejection, page 8, second paragraph).
Applicant argues in the paragraph spanning pages 9-10 of the Office Action, it is asserted that a "variant of SEQ ID NO:90 having at least 90% identity would have -2 nucleic acid (NA) changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 90 anywhere in the sequence in any combination." Applicant respectfully submits that in CRISPR-Cas systems, target recognition and cleavage allow several mismatches between the spacer and the target. See at least page 68, lines 1-15 of the specification, which describes spacers having one, two, three, four, or five mismatches as compared to the target nucleic acid. Applicant argues, accordingly, one of ordinary skill in the art would understand that Applicant was in possession of a guide comprising a spacer as claimed (Response to Rejection, page 8, last paragraph).
Regarding argument on spacers having one, two, three, four, or five mismatches, since applicant does not have examples it is not clear whether such spacers with mismatches would work for SGR1 and SGR2 genes, since some function changes would have been associated with the specific motif changes for example Jiao et al. page 7, left last paragraph teaches RY motif with “CATGCA” in promoters of SGR1 and SGR1 and ABRE motifs which would have been required to be changed in specific positions to have functional changes in the coding region, therefore applicant has not described that any of the changes in the 2 nucleotides (i.e. 90% identity) of the recited spacer sequence as SEQ ID NO:90 would have described functional changes showed by applicant as increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention.
Applicant argues at page 11 of the Office Action, it is asserted that Guo et al. (Proc. Nat. Acad Sci. USA, 101(25):9205-9210, 2004) teaches "that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated." Applicant argues in addition, it is asserted that Rodriguez-Leal et al. (Cell 171 :470-480, 2017) teaches "deletion of different sizes of conserved region (i.e. CRl, CR2 etc.) in SlCLV3 promoter in different species of tomato ... provides continuum of locule number variation where relative expression of SICL V3 is reduced in for example in m6 and m3 where there is no changes in m 12 and m8." Applicant respectfully points out that Guo et al. describe the tolerance of human 3-methyladenine DNA glycosylase (AAG) to amino acid substitutions and Rodriguez-Leal et al. describe deletions in the SlCL V3 promoter of tomato. Applicant argues the teachings of Guo et al. and Rodriguez-Leal et al. are of no relevance to the nucleotide or amino acid sequences of soybean SGR1 or SGR2 as these references describe different genes (AAG and SlCLV3) from different species (human and tomato). Applicant argues thus, Guo et al. and Rodriguez-Leal et al. do not provide a basis for concluding a lack of written support for soybean SGR1 or SGR2 sequences as claimed. Applicant argues as noted above, Jiao et al. show that one of ordinary skill in the art was well aware of the SGR genes in plants, including homologs, and the protein motifs encoded by the same. Applicant argues placed in this context, Applicant's specification provides sufficient guidance such that one of skill in the art would recognize that Applicant had possession of the full scope of the claimed invention at the time of filing (Response to Rejection, page 9, first paragraph).
Regarding argument on Guo et al. and Rodriguez-Leal et al. described genes from human and tomato plants are not found persuasive since the Guo showed that the method of mutation in random 10% of the amino acids and nucleotides leading to variants with 90% identities could produce inactive protein with any functions. Furthermore, Rodriguez-Leal et al. is clear to show that for the increase or decrease in expression of an associated gene specific mutational changes in specific promoter region of the gene are needed and some mutation causes increase, other causes decrease and other do not have effect to the expression of the gene at all. Furthermore, applicant’s example also showed various changes in expression when SGR1 and SGR2 genes were targeted in different regions of promoter. Therefore, a skilled in art would not be able to readily predict function of nucleic acid which has at least 90% identity to SEQ ID NOs: 75-82, and 90 and amino acid sequence having at least 90% sequence identity to SEQ ID NO: 83 and it is impossible to predict such a broad sequence variation will have any required function. Furthermore, applicant has not showed that the Applicant has not described any mutation in the promoter of SGR1 or SGR2 would significantly increases disease resistance also showed by Applicant’s Figures 4, 6 and 7.
Applicant argues the office Action further asserts that the Applicant has not described any deletion in the promoter of SGR1 or SGR2 that significantly increases disease resistance. See Office Action, pages 12. Applicant argues the Office Action primarily focuses on the CE35915 mutant, which is suggested to exhibit similar disease resistance to non-transformed controls. See Office Action, pages 12-15. Applicant respectfully points out "[i]t is not necessary that every permutation within a generally operable invention be effective in order for an inventor to obtain a generic claim, provided that the effect is sufficiently demonstrated to characterize a generic invention." Capon v. Eshhar, 418 F.3d 1359 (Fed. Cir. 2005). Applicant argues here, the specification provides a representative number of examples of soybean plants comprising at least one cell having a mutated endogenous SGR1 gene and a mutated endogenous SGR2 gene produced by the method as claimed, which exhibit an increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention as compared to a control soybean plant or plant part thereof, thereby demonstrating possession of the method as claimed. Applicant argues in particular, Table 1 shows that mutations were introduced into 15 different locations of the promoter of SGR1 (Response to Rejection, page 9, last paragraph) (positions 1036, 1238, 1240, 1243, 1249, 1362, 1862, 1871, 1873, 1884, 1894, 1940, 1942, 2006, and 2115), which included deletions of between 5 and 330 nucleotides in length, and mutations were introduced into 14 different locations of the promoter of SGR2 (positions 692, 1355, 1356, 1357, 1477, 1529, 1833, 1839, 1849, 1852, 1863, 1871, 1873, and 2149), which included deletions and insertions of between 4 and 1147 nucleotides in length. Applicant argues in addition, plants produced by the claimed method, which comprised combinations of SGR1 and SGR2 promoter mutations, were analyzed and at least seven were shown to exhibit an increase in chlorophyll retention levels during a soy rust infection time course (FIG. 6), a decrease in disease severity (FIG. 7), and delayed senescence (FIG. 4) as compared to non-transformed control plants. Applicant argues these results are sufficient to demonstrate to one of ordinary skill in the art that Applicant possessed the method as claimed at the time of filing (Response to Rejection, page 10, first paragraph).
Applicant argues the Office Action asserts that "Applicant has not described penetrance of any phenotype in a heterozygous organism therefore applicant has not described semidominant mutation of the endogenous SGR1 and SGR2 genes." See Office Action, page 15. Applicant respectfully points out that claim 1, and claims depending therefrom, do not require that the method produces a soybean plant or plant part thereof comprising at least one cell having “semi-dominant mutation." Therefore, the assertions in the Office Action are not relevant to the method as claimed (Response to Rejection, page 10, second paragraph).
Applicant argues with the regard to the Office Action's assertions regarding the significance of Applicant's exemplary mutants, Applicant points out that when modifying crop traits, particularly for desired resistance traits, even minor incremental changes in resistance can result in substantial improvements in overall crop yield, making these modifications agronomically significant. Applicant argues for example, delayed senescence and/or an increase in chlorophyll retention, in particular in the presence of a pathogen, can allow for increased photosynthetic efficiency, which in turn can increase yield per acre. Applicant argues in this respect, plants such as CE35902, CE39930, CE40104, CE35706, CE35816, CE39811, and CE35683, which comprise a mutation in the promoter of the SGR1 and SGR2 genes and a decrease in senescence and increase in chlorophyll retention compared to a control, may be readily propagated and used to generate a population of plants that collectively exhibit an overall increase in crop yield. Applicant argues accordingly, the Office Action's assertions regarding the CE35915 mutant do not diminish the significance of the results shown for the other mutants in the application (e.g., in FIGS. 4-8) and fail to provide a sufficient showing that the disclosure is not representative of the claimed genus (Response to Rejection, page 10, last paragraph).
Applicant argues in addition, at page 15 of the Office Action it is asserted that "Applicant has not described guide nucleic acid that binds to either only one of SGR1 gene would mutate endogenous SGR1 and SGR2 genes located in different chromosomes." Applicant argues claim 12 is amended herein to recite that the gene editing system comprises a guide nucleic acid comprising a spacer that binds to a portion of the promoter region of the endogenous SGR1 gene and a guide nucleic acid comprising a spacer that binds to a portion of the promoter region of the endogenous SGR2 gene; or a guide nucleic acid comprising a spacer that binds to a portion of the promoter region of the endogenous SGR1 gene and a portion of the promoter region of the endogenous SGR2 gene, thereby addressing the rejection as applied to claim 12. Applicant argues support for this amendment may be found at least in FIGS. 2-3 and Table 2, which show the design of guide nucleic acids with spacers that are specific to SGR1 or spacers that are specific to SGR2 and guide nucleic acids with spacers that target both SGR1 and SGR2.
Regarding argument on claim 1 does not require comprising at least one cell having “semi-dominant mutation." and since applicant has cancelled claim 5 the argument was found persuasive.
Regarding argument on amendment of claim 12 to recite guide nucleic acid comprise spacer for SGR1 and SGR2 or both SGR1 and SGR2 is found persuasive, therefore the part of written description rejection has been withdrawn.
Claim Rejections - 35 USC § 102
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.
Anticipated by Chang et al.
Claim 14 is rejected under 35 U.S.C. 102 (a) (1) as being anticipated by Chang et al. (Published: 2019, Journal: Plant Physiology, 180: 711–717), further evidenced by Lipman et al. (US Publication Number: US 2020/0199604 A1, Publication date: June. 25, 2020).
Following analysis is modified to address the applicant’s amendment of claim 14 lines 1 and 2 to recite “the promoter region of” an endogenous SGR gene
Claim recites a guide nucleic acid that binds to sequence having at least 90% sequence identity to SEQ ID NOs: 81 or 82 and any one of SEQ ID NOs: 75-80.
Regarding claim 14, Chang et al. teaches primer sequences (i.e. nucleic acid sequence) in Supplemental Table S4 with range of nucleic acid fragment from GmSGR1 and GmSGR2 genes, for example “GGAGCCACCATTACAAGCG” has 100% sequence identity to SEQ ID NO:75 and 81. Thus the sequence would bind to the SGR1 gene. Furthermore, the sequence is a guide nucleic acid since the first two nucleotides “GG” would have been used as Protospacer Adjacent Motif (PAM) sequence for Cas9. See for example Lippman et al. showed the evidence that “NGG” where N can be any other nucleotide is a PAM sequence for Cas9 nuclease in a guide RNA (page 16, paragraph 0083).
Alignment of Chang et al.’s primer “GGAGCCACCATTACAAGCG” to the SEQ ID NO: 75:
Query: None Query ID: lcl|Query_8062113 Length: 19
>
Sequence ID: Query_8062115 Length: 2298
Range 1: 1946 to 1964
Score:35.6 bits(38), Expect:5e-07,
Identities:19/19(100%), Gaps:0/19(0%), Strand: Plus/Plus
Query 1 GGAGCCACCATTACAAGCG 19
|||||||||||||||||||
Sbjct 1946 GGAGCCACCATTACAAGCG 1964
Furthermore, SEQ ID NO:75 is a UTR region as defined as “untranslated regions of SGR genomic sequences as described herein (e.g., SEQ ID N0:75 or SEQ ID N0:76) (pages 18 and 19, last and first paragraph). There the region is a portion of the promoter region.
Response to Argument
Applicant's arguments filed 10/21/2025 have been fully considered but they are not persuasive.
Applicant argues the cited primer sequence of Chang was used in a PCR reaction to amplify genomic DNA encoding GmSGR1. See, Chang, Supplemental Methods, lines 51-58. Applicant submits that a primer is not, nor would it be construed by one of ordinary skill in the art to be, a guide nucleic acid. Applicant argues the specification (and general knowledge in the art) specifies that a guide nucleic acid has at least two components, namely at least one spacer sequence that is complementary to (and hybridizes to) a target DNA and at least one repeat sequence (e.g., of a CRISPR-Cas system). See, e.g., the paragraph spanning pages 65 and 66 of the specification. Applicant argues there is no additional sequence associated with the primer of Chang that would constitute a repeat sequence. Applicant argues therefore, Chang fails to teach a guide nucleic acid as claimed.
Applicant's arguments filed have been fully considered but they are not persuasive since applicant defines “A "guide nucleic acid," "guide RNA," "gRNA," "CRISPR RNA/DNA" "crRNA" or "crDNA" as used herein means a nucleic acid that comprises at least one spacer sequence, which is complementary to (and hybridizes to) a target DNA (e.g., protospacer), and at least one repeat sequence (e.g., a repeat of a Type V Cas12a CRISPR-Cas system, or a fragment or portion thereof; a repeat of a Type II Cas9 CRISPR-Cas system, or fragment thereof; a repeat of a Type V C2c 1 CRISPR Cas system, or a fragment thereof; a repeat of a CRISPR-Cas system of, for example, C2c3, Cas12a (also referred to as Cpfl), Casl2b, Cas12c, Casl2d, Cas12e, Cas13a, Cas13b, Cas13c, Cas13d, Casl, CaslB, Cas2, Cas3, Cas3', Cas3", Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csx12), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, C1m·3, Crm4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csx16, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4 (dinG), and/or Csf5, or a fragment thereof), wherein the repeat sequence may be linked to the 5' end and/or the 3' end of the spacer sequence” (Spec, page 64 and 66). Therefore the main component is a spacer sequence that is complementary to SGR1 or SGR2 and repeat sequence would comprise a fragments of repeat of for example of Cas9 wherein since fragment of the repeat sequence could be any sequence. For example applicant defines “As used herein with respect to nucleic acids, the term "fragment" or "portion" refers to a nucleic acid that is reduced in length relative (e.g., reduced by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 340, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, or 900 or more nucleotides or any range or value therein) to a reference nucleic acid and that comprises, consists essentially of and/or consists of a nucleotide sequence of contiguous nucleotides identical or almost identical (e.g., 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical) to a corresponding portion of the reference nucleic acid (page 16, lines 4-13). Therefore it is not clear what does it mean to be “consists essentially of” or “almost identical” in the fragments of repeat sequence of any of a CRISPR-cas effector protein therefore the repeat sequence would have been any sequence few to many sequences in the disclosed sequence of Gao et al. for example it the sequence was required by any of the larger numbers of 340 -900 or more or any range or value therein. This would lead to some fragments which would be as small as single nucleotides. This makes the main components of guide RNA is spacer sequence and PAM sequences that is discloses by Chang et al. wherein the 90% identity would allow small fragment to be associated with the guide RNA.
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Obvious over Chang et al. and further in view of Gao et al. and Lippman et al.
Claims 1-11, 13 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Chang et al., and further in view of Gao et al. (Published: 2016, Journal: Molecular Plant 9: 1272–1285) and further in view of Lippman et al. (WIPO International Pub. No.: WO 2018/213547 A1, publication date: 22 November 2018).
Following analysis is modified to analyze the newly added claim 16 and the references to page numbers and line numbers are modified to cite the WIPO version of Lippman et al. which has same evidence as the US Patent application Pub. No.: US 2020/0199604 Al, publication date: 06/25/2020 version, see below.
Claims are drawn to a method of producing a soybean plant comprising mutated endogenous genes SGR1 and SGR2 with a gene editing system wherein the mutation is generated in the promoter region of the genes.
Regarding claims 1, 4, 10-11 and 16, Chang et al. teaches the SDS foliar chlorosis was lowest in the mutant genotype wherein expression level of the GmSGR1 and GmSGR2 increases post inoculation (page 714, Figure 2), the increase was higher for LD01-5907 (wild type) compared to the mutant soybean variety Soybean variety GD2422 (d1d1d2d2 genotype) the mutant Soybean variety GD2422 (d1d1d2d2 genotype) maintained its relative chlorophyll content (see Figure 3 below). Therefore, lower expression of the GmSGR1 and GmSGR2 is associated with stay green trait in the mutants.
Chang et al. teaches GmSGR1 (as D3) (Glyma.11G027400) and GmSGR2 (Glyma.01G214600) (as D1) are the STAY-GREEN gene, were found in SoyBase used in their study (page 713, right first paragraph, Supplemental Figure S3) which is the same gene as applicant described as their wildtype genes see Spec, page 76, Table 1 as locus 37 and locus 38 as SGR2 and SGR1 genes as SEQ ID NOs: 76 and 75. Furthermore, NCBI BLAST sequence alignment of the SGR protein elected as SEQ ID NO: 73 and 74 shows 100% sequence identity t0 a D2 and D1 (senescence-inducible chloroplast stay-green protein) of soybean (Glycine max) (see enclosed PDF) which are applicant described SGR1 and SGR2 genes.
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Gao et al. teaches NYE1/SGR1 is key regulator of chlorophyll catabolism in diverse plant species (page 1272, Abstract) wherein the mutation in the ABRE motifs of the truncated promoter sequence in Arabidopsis NYE1/SGR1 genes showed significant difference in the ABA responsiveness for the expression of the NYE1/SGR1 genes (see Figure 1 below, page 1275, left first paragraph). Gao et al. teaches ABRE consensus motif A1 core G-box motif (CACGTG) such motif are present in both Applicant’s SEQ ID NOs: 75 and 76 (see sequence listings).
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Chang et al. and Gao et al. does not teach the mutation is created by contacting a target site in the promoter region of an endogenous SGR1 and SGR2 genes with a gene editing system comprising a nuclease comprising a cleavage domain and a nucleic acid binding domain binding to the SGR1 and SGR2 genes.
Lippman et al. teaches cis - regulatory elements in gene promoters present an exciting target for creating new, weak alleles with the ultimate goal of modulating crop yield traits (page 66, lines 11-12). Lipman et al. teaches gene editing using CRISPR/Cas9 technology to produce genetic variation that changes the expression -hence the activity of a single gene in a controlled and directed manner wherein the technology can be used to target specific sets of genes with major effects, taking advantage of genomic information regarding the developmental patterns and genes controlling yield traits, pathogen resistance etc. (page 87, lines 1-12). Lipman teaches the method would be used in soybean (page 34, lines 14-18). Lipman et al. teaches an example of a method of generating mutated promoters using CRISPR/Cas9 (i.e. a gene editing system comprising a nuclease comprising a cleavage domain) and eight sgRNAs (i.e. a gene editing system comprising a nucleic acid binding domain) in tomato plant targeting upstream of the transcriptional start site in SlCLV3 gen, wherein the DNA sequencing revealed modification in the transcriptional expression of the gene and range of new phenotypes (page84, lines 23-26, page 85, lines 1-7, See figure 3below). Thus, such method would produce in a soybean plant a mutation in cis-regulatory elements in gene promoters that would change expression of the gene leading to phenotype changes.
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Hence it would have obvious to someone skill in art from teaching, suggestion and motivation from Chang et al. for a method of altering the expression of the SGR1 and SGR2 for modulation of disease resistance and stay green trait in soybean, furthermore teaching from Gao et al. that the targeting of the promoter region of SGR gene would alter the expression of the SGR gene leading to the change in stay green traits, someone skilled in the art would have carried out by the method described by Lippman et al. to target specific region of the promoters and screen for mutation leading to the change in stay green traits in the soybean plant. Someone skilled in the art would combine arts to develop a recited method for producing a soybean plant comprising at least a mutated endogenous SGR1 and SGR2 gene.
Regarding claim 2, Chang et al. teaches the SDS foliar chlorosis was lowest in the mutant genotype wherein expression level of the GmSGR1 and GmSGR2 increases post inoculation (page 714, Figure 2), the increase was higher for LD01-5907 (wild type) compared to the mutant soybean variety Soybean variety GD2422 (d1d1d2d2 genotype) the mutant Soybean variety GD2422 (d1d1d2d2 genotype) maintained its relative chlorophyll content (see Figure 3 below). Therefore, the mutant had delayed senescence or had longer chlorophyll retention.
Regarding claim 3, CRISPR Cas9 cleaves the endogenous genes. Furthermore, Chang et al. teaches endogenous SGR1 and SGR2 genes in soybean.
Regarding claim 5, Applicant defines “A "semi-dominant mutation" refers to a mutation in which the penetrance of the phenotype in a heterozygous organism is less than that observed for a homozygous organism.” (page 11, lines 29-30). Since Chang et al., Gao et al. and Lippman et al. teaches the expression changes in the genes by mutating promoters are quantitative in nature, such changes would have been semi-dominant by their nature.
Regarding claims 6-9, Lipman et al. teaches CRISPR Cas9 induced mutation are deletion, insertion etc. (page15, paragraph 0077) or combination of the mutation. A combination of deletion and insertion would equivalent to at least a substitution and that would be for a, G, C or T.
Regarding claim 13, the plant would have been the obvious product of the obvious method of claim 1.
Response to Argument
Applicant's arguments filed 10/21/2025 have been fully considered but they are not persuasive.
Applicant argues at page 20 of the Office Action, Chang is said to teach that "lower expression of the GmSGR1 and GmSGR2 is associated with stay green trait in the mutants." Applicant argues at page 22 of the Office Action, Gao is said to teach that "the mutation in the ABRE motifs of the truncated promoter sequence in Arabidopsis NYE1/SGR1 genes showed significant difference in the ABA responsiveness for the expression of the NYE1/SGR1 genes." Applicant argues the Office Action acknowledges that Chang and Gao do not teach a mutation created by contacting a target site in the promoter region of an endogenous SGR1 and SGR2 genes with a gene editing system comprising a nuclease comprising a cleavage domain and a nucleic acid binding domain binding to the SGR1 and SGR2 genes. See Office Action, page 23. Applicant argues Lippman is suggested to compensate by describing "an example of a method of generating mutated promoters using CRISPR/Cas9 (i.e. a gene editing system comprising a nuclease comprising a cleavage domain) and eight sgRNAs (i.e. a gene editing system comprising a nucleic acid binding domain) in tomato plant targeting upstream of the transcriptional start site in SlCL V3 gen[e]." See Office Action, page 24(Response to rejection, page 12, paragraph 3).
Applicant argues Chang describes two soybean varieties (GD2422 and LD0l-5907), that exhibit a difference in foliar resistance to phytotoxins produced by Fusarium virgulifomre, which causes sudden death syndrome (SDS). Applicant argues in particular, whereas the GD2422 variety exhibits resistance to SDS foliar chlorosis, the LD01-5907 variety displays susceptibility to SDS foliar chlorosis. See Chang, page 713, paragraph spanning col. 1-2 (Response to rejection, page 12, last paragraph).
Applicant argues Chang shows that GmSGR1 and GmSGR2 expression in the LD01-5907 variety was significantly higher than expression of GmSGR1 and GmSGR2 in the GD2422 variety in response to phytotoxins produced by F. virgulifomre. See Chang, page 714, col. 1, paragraph 2. Applicant argues however, Chang does not conclude that resistance to SDS foliar chlorosis is attributed to lower expression of GmSGR1 and GmSGR2. Applicant argues rather, Chang attributes the phenotype to the dldld2d2 mutant genotype, which contains an insertion and exon duplication in the GmSGR1 gene (d2 allele) and a deletion of thymine that causes a frameshift in the exon of the GmSGR2 gene (di allele). See Chang, Figure 4 and page 713, col. 1, first paragraph and col. 2, last paragraph. Applicant argues importantly, the di and d2 mutations are within the coding sequence of GmSGR1 and GmSGR2. Applicant argues in addition, Chang does not teach or suggest that the d1d1d2d2 mutant was generated with a gene editing system nor does this reference teach or suggest producing a soybean plant or plant part thereof comprising at least one cell having a mutated endogenous SGR1 gene and a mutated endogenous SGR2 gene by targeting promoter region of GmSGR1 and GmSGR2 (Response to rejection, page 13, first paragraph).
Applicant agues Gao describes the identification of three abscisic acid (ABA)-responsive element binding transcription factors (ABF2, ABF3, and ABF4) that are capable of physically interacting with the NYE1/SGR1 promoter in Arabidopsis. See Gao, Figure lA and abstract. Applicant argues Gao describes truncations of the NYE1 promoter and the effect of the same on ABA-induced reporter protein (GFP) expression. See Gao, Figure lB. Applicant argues this reference also describes a staygreen phenotype of an abf2abf3abf4 triple mutant after ABA treatment. See Gao, Figure 2. Applicant argues Gao does not teach or suggest a method of producing a plant comprising a mutation in the promoter region of an endogenous NYE1 gene, or in the promoter of any endogenous gene, or a phenotype associated with the same (Response to rejection, page 13, second paragraph).
Applicant argues Lippman discloses promoters and cis-regulatory regions as targets for generating mutations that may affect crop yield. Applicant argues Lippman fails to teach or suggest the generation of a mutation in the promoter region of an endogenous SGR1 gene and an endogenous SGR2 gene, as claimed. Applicant argues notably, the use of CRISPR as disclosed in Lippman is random not directed to a particular target site (see at least: paragraph [0004] ("In particular, as described herein, a single CRISPR/RNA Guided endonuclease (e.g., CRISPR/Cas9) expression construct encoding multiple different guide RNAs can be used to generate multiple and different types of mutations within a regulatory region of a target gene. Applicant argues these different mutations to the target gene can produce a quantitative range of phenotypes from weak to strong."); paragraph [0178] in Example 1 ("Using the near-random nature of CRISPR/Cas9 mutagenesis as an advantage, an unbiased approach is used to identify plants carrying desirable promoter mutations."); see also Example 2, paragraph [0192] ("Notably, a range of weak to strong phenotypic effects was also observed, .... When compared to M82, fas and slclv3cR, four of the TO lines showed quantitative differences (FIG. 3E), implying the new alleles generated by CRISPR/Cas9 were able to produce a range of new phenotypic variation.") (Response to rejection, page 13, last paragraph).
Applicant argues both the method of targeting and the nature of the mutations as taught by Lippman would be considered by the ordinary skilled person to be entirely random and not directed as claimed herein (Response to rejection, page 14, first paragraph).
Applicant argues paragraph [0192] of Lippman, which the Examiner cites for teaching an example of a method of generating mutated promoters using CRISPR/Cas9, shows deletions in the promoter of a single gene, which is a different gene from that claimed (SICLV3 vs. SGR1 and SGR2), in a different plant than that claimed (tomato vs. soybean), and a completely different phenotype than that claimed (locule number and fruit size vs. increase in resistance to soybean rust, delayed senescence and/or chlorophyll retention). Applicant argues no evidence is provided that the methodology of Lippman when applied to two different promoters of two different genes in a different plant would provide a plant or plant part thereof in the manner claimed. Applicant argues at best, the guidance in Lippman directs the ordinary skilled person to randomly target 5' and 3' regions of a gene, for generating libraries of plants with mutated promoters, and screening for any changes that might result in a desired phenotype. Applicant argues Lippman fails to provide sufficient guidance such that one of ordinary skill would have had any reasonable expectation of successfully targeting a promoter region of both a SGR1 and a SGR2 gene of a soybean plant as claimed herein (Response to rejection, page 14, second paragraph).
Applicant argues as discussed above, the mutations described in Chang are within the coding sequence of GmSGR1 and GmSGR2, the mutations in the NYE1 promoter of Gao are in Arabidopsis and are not in the endogenous gene, and the mutations of Lippman are randomly inserted in the promoter of the SICLV3 gene in tomato. Applicant argues accordingly, when taken together, Chang, Gao and Lippman fail to teach or suggest targeting a promoter region of an endogenous SGR1 gene and an endogenous SGR2 gene of a soybean plant or plant part thereof. Applicant argues because Gao and Lippman describe mutations in different genes and in different plants than that of Chang, there would have been no motivation or rationale to combine the cited references (Response to rejection, page 14, second to last paragraph).
Regarding argument on Change et al. does not teach gene editing system to produce mutation in promoter region the argument was not found persuasive since the art teaches the SEQ ID NOs: 45 and 76 in soybean and it clearly teaches that the lower expression of the GmSGR1 and GmSGR2 is associated with stay green trait in the mutants. Furthermore, Gao et al. showed the predictable science that the specific deletion in promoter region leads to altered expression of the stay green genes.
Regarding argument on Lippman is random not directed to a particular target site, the argument was not found persuasive since applicant’s claim does not recite targeting specific region of promoter and does not require any functions changes except claim 2. Furthermore, Lippman et al. teaches their sgRNA are target putative regulatory region of a gene within 5 kb upstream or downstream of the coding sequence (page8, paragraph 0057), the sgRNA are complementary to a target sequence within a target region (page 10, paragraph 0062), Furthermore, Lippman et al. teaches in FIGs. 2C-2F is a diagram showing that CRISPR-Cas9 targeting the region downstream of WUS containing the le motif in S.pim and S.lyc disrupted a putative AGAMOUS binding site (CArG) using specific sgRNA leading to increase in locule numbers in fruits (page7, paragraph 0043).
Therefore Change et al. and further in view of Gao et al. and Lippman et al. showed the targeting promoter region would alter expression of a stay green genes SGR1 and SGR2 leading to predictable change in function for example alteration of senescence process. Furthermore, applicant does not recite any function changes except claim 2 and recite targeting any site of a promoter region leading to mutated SGR1 and SGR2 gene with any genomic structure.
Furthermore, where a rejection of a claim is based on two or more references, a reply that is limited to what a subset of the applied references teaches or fails to teach, or that fails to address the combined teaching of the applied references may be considered to be an argument that attacks the reference(s) individually. Where an applicant’s reply establishes that each of the applied references fails to teach a limitation and addresses the combined teachings and/or suggestions of the applied prior art, the reply as a whole does not attack the references individually as the phrase is used in Keller and reliance on Keller would not be appropriate. This is because the test for obviousness is what the combined teachings of the references would have suggested to a person having ordinary skill in the art (PHOSITA).”
Conclusion
No claim is allowed.
Claims 12 and 15 are free of prior art. closest prior art is Gao et al. which does not expressly teach spacer sequence SEQ ID NO:90 binding to the SGR1 and SGR2 leading to mutation of the SGR1 and SGR2 by a nuclease. Furthermore, Gao et al. does not teach guide nucleic acid which would also comprise repeat sequence (see definition above) and comprise SEQ ID NO:90. There is no specific teachings to choose sequence of SEQ ID NO:90 as spacer sequence in the method of mutating a soybean plant and making it a guide nucleic acid.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/SANTOSH SHARMA/ Examiner, Art Unit 1663
/DAVID H KRUSE/ Primary Examiner, Art Unit 1663