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 .
Claim Status
Claims 1-14 are pending and are examined in this office action.
Specification
The disclosure is objected to because of the following informalities: Tables on pages 70 and 71, do not have a table number, applicant are advised to add table numbers and renumber the remaining tables.
Appropriate correction is required.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable codes in page 74, lines 2 and 8. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable codes; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
101, 102 claim 1 at least one amino acid would mean any more deletions and insertions.
Claim Objections
Claim 1 is objected to because of the following informalities:
In claim 1 step (a), the claim recites the phrase “given under” which is advised to recite instead the term “of” to clearly recite the nucleic acid encodes SEQ ID NO:2.
In claim 6 last line, claim recite the phrase “of the complement” is grammatically incorrect and applicants are advised to correct it to delete the extra term “of” from the line.
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 1-14 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.
Breadth of the Claim
Any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 are required to cause increase in number of secondary branches.
Any complementary sequence of SEQ ID NO:6 that would encode SEQ ID NO:2 would encompass large variants of sequences of SEQ ID NO:6 (claim 1 step b)) since complementary sequence could be fully or partially complementary.
The nucleotide sequence variants that encode SEQ ID NO:2 comprise large number of variants of nucleic acid sequences (claim 1 step a)).
The increased average number of secondary branches would be any increase since applicant does not recite any control or standard to compare (claims 1 and 4).
The SEQ ID NO:6 or SEQ ID NO:2 that comprises nucleotide insertion, duplication, deletion or replacement resulting in mutants with one or more amino acids insertion, duplication, deletion or replacement comprise large variants of nucleic acid or proteins (claim 5).
Any of the allele specific primers or probes that has at least 10 nt or 15 of SEQ ID NO:6 or the complement strand of SEQ ID NO:6 (claims and 6, 9 and 11).
The nucleic acid hybridization making use of CLD14 would produce large number of variants of polynucleotides.
Any pair of PCR primers or at least one oligonucleotide probe, which primers or oligonucleotide probe comprise at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or more consecutive nucleotides of the genomic allele of the ClD14 gene would hybridize to the large variants of genomic allele and/ or amplify part large variants of the genomic allele in a PCR assay (claims 12 and 13).
Any codon insertion, codon change, codon deletion or codon change to STOP codon in anywhere in the coding region of the allele in the mutant allele (claim 7) would comprise large variants with various functions.
What is Described in the Specification
Applicant describes the following:
QTL mapping for secondary branching (also referred to as 'multi branching') was done on an F2 population developed by crossing the multi branching variety Sidekick F1 with a proprietary normal branching watem1elon plant (Response to Rejection, page 70, lines 1-3).
It was found that a gene on chromosome 8 caused the multi branching phenotype in Sidekick F1 (page 70, line 7).
The gene ClD14, contained a duplication of 24 nucleotides, which encoded 8 additional amino acids compared to the wild type gene, present in the normal-branching parent (page 70, lines 7-9).
The multibranching phenotype, as only seen when the mutant allele of the gene (comprising the 24-nudeotide duplication) was present in homozygous form (page 70, lines 9-11, Table in page 17).
watermelon TTLLING population was screened, and several mutants were found in the ClD 14 gene leading to amino acid substitutions or STOP codons (page 72, lines 25-27).
The W155Stop mutant has a multibranching phenotype, when the mutation is in homozygous form (W155*/W155*), the phenotype looks like that of the original mutant (ClD14ins/ClD14ins), comprising the duplication of 8 amino acids (page 73, lines 2-4).
ClD14ins mutant allele must be encoding a non-functional protein, which does not transmit the signal to suppress secondary branching leading to full multibranching" or 'strong multibranching" (page 74, lines 2-7).
Difference Between What was Described and What is Claimed
Applicant has not described at least any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 would cause increase in number of secondary branches other than the homozygous W155Stop/ W155Stop of SEQ ID NO:2 leading to SEQ ID NO:5.
Applicant has not described any complementary sequence of SEQ ID NO:6 that would encode SEQ ID NO:2 other than SEQ ID NO:6 itself (claim 1).
Applicant has not described mutants of all the nucleotide sequence variants that encodes SEQ ID NO:2 other than SEQ ID NO:6.
Applicant has not described the increased average number of secondary branches as compared to what control or standard (claims 1 and 4).
Applicant has not described use of any mutant allele of SEQ ID NO:6 or SEQ ID NO:2 that comprises nucleotide insertion, duplication, deletion or replacement resulting in mutants with one or more amino acids insertion, duplication, deletion or replacement (claim 5).
Applicant has not described any of the allele specific primers or probes that has at least 10 nt or 15 nt of SEQ ID NO:6 or the complement strand of SEQ ID NO:6 (claims 6, 9 and 11).
Applicant has not described nucleic acid hybridization conditions to develop the oligonucleotide probes or oligonucleotide product (claim 5, 11 and 12).
Applicant has not described any pair of PCR primers or at least one oligonucleotide probe, which primers or oligonucleotide probe comprise at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or more consecutive nucleotides of the genomic allele of the ClD14 gene and can hybridize to the genomic allele and/ or amplify part of the genomic allele in a PCR assay (claims 12 and 13).
Applicant has not described any codon insertion, codon change, codon deletion or codon change to STOP codon in anywhere in the coding region of the allele in the mutant allele (claim 7).
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.
Claim 1 recite a watermelon plant or part or seed comprising at least one of the amino acid deletion or replacement with different amino acid in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259. Thus, the structure of the watermelon plant genome can be any plant with such any of the deletions and replacement with different amino acids. The claims allow large number of deletions and combinations of deletions or replacement of amino acids. Instead, applicant has only showed a 8 amino acids insertions at position 93 of wildtype (i.e. SEQ ID NO:2) causes multibranching phenotype in Sidekick variety as compared to the wildtype control.
Furthermore, the increased average number of secondary branches would have been any increase since the claims 1 and 4 do not recite any standard or control plant to compare for increase. For example, Mohanta et al. (Published: 2016, Journal: Journal of Crop and Weed, 12(3):175-177) teaches in the sample of thirteen watermelon verities the branch numbers varied from 4-6 (page 17, paragraph 2, page, page 176, table1). Therefore, it is not clear what modification in the watermelon genome would cause which level of increase in branch numbers.
Therefore, there is dearth of description of increased average number of secondary branches as compared to what control or standard (claims 1 and 4).
Specific motif or domain of the protein would have to be targeted to have desired effect of increase in branch number in watermelon. For example, Guo et al. (Nature Published:2012, Communications 4:1566 DOI: 10.1038/ncomms2542, pages 1-12) teaches CArG-box motifs (Os03g10620) [C(A/T)TTAAAAAG] found in promoter of D14 in rice controls the tiller development (page 6, right paragraph 2). Furthermore, Kagiyama et al. (Published: 2013, Journal: Genes to Cells 18: 147–160) teaches different D14 genes in rice and Arabidopsis comprise various domains (page 149, Figure 2).
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Lee et al. (Published: 2026, Journal: J. Integr. Plant Biol. 68: 113–129) teaches different conserved motifs are present in the D14 gene orthologs (see supplementary figure S1). Therefore, specific motif would cause various effect on the change in the function of the gene.
Hu et al. (Published: 2017, Journal: Rice. Front. Plant Sci. 8:1935. doi: 10.3389/fpls.2017.01935) teaches hydrolase activity of D14 is essential for the SL-induced D14 degradation wherein the S147A and H297Y transgenic plants exhibited high tillering phenotypes showing both are indispensable for the signal perception of SLs in vivo (page6, right first paragraph). Hu et al. teaches when created mutation in lysine sites as K33, K55, K166, K246, and K280, the degradation of GFP in D14K55E-GFP, D14K166E-GFP or D14K246E-GFP was relatively unaffected (Figure 2C) wherein K280 be the key amino acid for SL induced D14 degradation (pages 5 and 6, last and first paragraphs). Hu et al. teaches D14 degradation is a complex process including many other components (see Figure 6). Therefore, specific mutation would be required to cause the phenotype of increased branching numbers. Instead, applicant has not described increase in branching number in any other plant other than W155Stop / W155Stop of SEQ ID NO:2 and 8 amino acids insertions at position 93 of wildtype (i.e. SEQ ID NO:2). Therefore, there is dearth of description of at least any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 would cause increase in number of secondary branches other than the homozygous W155Stop / W155Stop of SEQ ID NO:2 leading to SEQ ID NO:5.
Furthermore, there is dearth of description of any codon insertion, codon change, codon deletion or codon change to STOP codon in anywhere in the coding region of the allele in the mutant allele (claim 7) other than the homozygous W155Stop / W155Stop of SEQ ID NO:2 leading to SEQ ID NO:5. Specification page 72, Table 2 showed mutation in codon wherein the change in phenotype to multibranching has only been described in the TGG (W), TAG (Stop) or W155Stop.l. There are no recorded changes in the other codons.
Applicant has not described any complementary sequence of SEQ ID NO:6 that would encode SEQ ID NO:2 other than SEQ ID NO:6 itself (claim 1). The degree of complementarity of a sequence would comprise both fully complementary where every base pairs perfectly and partially complementary where only sections of the strand match or mismatches. Therefore, there would be large number of sequences that would have various complementarity to SEQ ID NO:6 which is 893 nucleotides long. Therefore, there is dearth of description of any complementary sequence of SEQ ID NO:6 that would encode SEQ ID NO:2 (claim 1).
Applicant has not described all the mutants of the nucleotide sequence variants that encodes SEQ ID NO:2 other than SEQ ID NO:6 itself. This is because of the degeneracy of genetic code and potential many alternative nucleotide sequences and each protein could have been encoded by numerous distinct nucleotide sequences because of synonymous codons. Therefore, there is dearth of description of the mutant sequences of any of the nucleotide sequences and their variants wherein the nucleotide sequence originally encodes SEQ ID NO:2.
Applicant has not described use of any mutant allele of SEQ ID NO:6 or SEQ ID NO:2 that comprises nucleotide insertion, duplication, deletion or replacement resulting in mutants with one or more amino acids insertion, duplication, deletion or replacement (claim 5). The mutation in ClD14 with any number of insertions, duplication and deletion would produce many mutant ClD14 mutants in watermelon plant that would may not have any effect on the phenotype of the plants. Therefore, the is dearth of description use of detecting or selecting such a broad population of plant with many variants of the plant without predictable results in effect on the phenotype to of the plants with any insertions, deletion and mutation in SEAQ ID NO:6 or SEQ ID NO:2.
Applicant has not described any pair of PCR primers or at least one oligonucleotide probe, which primers or oligonucleotide probe comprise at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or more consecutive nucleotides of the genomic allele of the ClD14 gene and can hybridize to the genomic allele and/ or amplify part of the genomic allele in a PCR assay (claims 12 and 13). It is known in the art that too short primers, having fewer than 17 nucleotides, produce inaccurate or non-specific binding. Too short primer would anneal non-specifically to the several position on the DNA strand, which result in non-specific binding. For example, Rocha et al. (Published: 2004, Journal: In Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering (pp. 149-155). IEEE, teaches that primers having length of 17 bases or longer are sequence specific, and the likelihood of annealing to sequence other than the chosen target is very low even in the large genome size of human or maize (about 4 billion bases) (Page 3, section 3.3 Primer Length). Therefore, there is dearth of description of the short primers would be useful for effectively selecting in method of generating PCR amplification product or method of hybridizing the part of the genomic DNA of watermelon plant.
The nucleic acid hybridization making use of CLD14 would produce large number of variants of polynucleotides. Applicant has not described the specific hybridization oligonucleotides that would effectively hybridize with the mutated SEQ ID NO:6 or fragments of SEQ ID NO:6 (claims 5, 11 and 12).
"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.
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 has described the structure of claimed genus to have application as recited function at the time this application was filed.
Claim Rejections - 35 USC § 112 – Scope of Enablement
Claims 1-4 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the watermelon plant or plant part or a watermelon seed comprising a mutant allele of a gene named ClD14 (Citrullus lanatus Dwarf14), wherein the mutant allele encodes a protein in which the codon for amino acid 155 is replaced by a stop codon wherein the mutant allele results in the plant developing an increased average number of secondary branches when the mutant allele is in homozygous form as compared to control plant, does not reasonably provide enablement for the watermelon plant or plant part or a watermelon seed comprising mutant allele encodes a protein in which the codon for amino acid 255 is replaced by a stop codon or the mutant encodes a protein wherein any of the amino acid is replaced by different amino acid or any amino acid is missing at position 22 to 259 of SEQ ID NO:2. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e., commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
The Breadth of the Claims and nature of invention:
Any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 are required to cause increase in number of secondary branches.
Any complementary sequence of SEQ ID NO:6 that would encode SEQ ID NO:2 would encompass large variants of sequences of SEQ ID NO:6 (claim 1 step b)) since complementary sequence could be fully or partially complementary.
The nucleotide sequence variants that encode SEQ ID NO:2 comprise large number of variants of nucleic acid sequences (claim 1 step a)).
The increased average number of secondary branches would be any increase since applicant does not recite any control or standard to compare (claims 1 and 4).
The amount of direction provided by the inventor:
The gene ClD14, contained a duplication of 24 nucleotides, which encoded 8 additional amino acids compared to the wild type gene, present in the normal-branching parent (page 70, lines 7-9).
The multibranching phenotype, as only seen when the mutant allele of the gene (comprising the 24-nudeotide duplication) was present in homozygous form (page 70, lines 9-11, Table in page 17).
The watermelon TTLLING population was screened, and several mutants were found in the ClD 14 gene leading to amino acid substitutions or STOP codons (page 72, lines 25-27).
The W155Stop mutant has a multibranching phenotype, when the mutation is in homozygous form (W155*/W155*), the phenotype looks like that of the original mutant (ClD14ins/ClD14ins), comprising the duplication of 8 amino acids (page 73, lines 2-4).
Applicant states “Q255* may result in a loss of function” (page 9, lines 28-29).
Applicant Table 2 states the plant comprise the heterozygous plant with Q255 Stop of the dwarf 14 wherein applicant does not teach which phenotype is produced with the Q255stop.
The state of the prior art:
Specific motif or domain of the protein would have to be targeted to have desired effect of increase in branch number in watermelon. For example Guo et al. teaches CArG-box motifs (Os03g10620) [C(A/T)TTAAAAAG] found in promoter of D14 in rice controls the tiller development (page 6, right paragraph 2). Furthermore, Kagiyama et al. teaches different D14 genes in rice and Arabidopsis comprise various domains (page 149, Figure 2).
Lee et al. teaches different conserved motifs are present in the D14 gene orthologs (see supplementary figure S1). Therefore, specific motif would cause various effect on the change in the function of the gene.
Hu et al. teaches hydrolase activity of D14 is essential for the SL-induced D14 degradation wherein the S147A and H297Y transgenic plants exhibited high tillering phenotypes showing both are indispensable for the signal perception of SLs in vivo (page6, right first paragraph). Hu et al. teaches when created mutation in lysine sites as K33, K55, K166, K246, and K280, the degradation of GFP in D14K55E-GFP, D14K166E-GFP or D14K246E-GFP was relatively unaffected (Figure 2C) wherein K280 be the key amino acid for SL induced D14 degradation (pages 5 and 6, last and first paragraphs). Hu et al. teaches D14 degradation is a complex process including many other components (see Figure 6). Therefore, specific mutation would be required to cause the phenotype of increased branching numbers. Instead, applicant has not described increase in branching number in any other plant other than W155Stop / W155Stop of SEQ ID NO:2. Therefore there is dearth of description of at least any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 would cause increase in number of secondary branches other than the homozygous W155Stop / W155Stop of SEQ ID NO:2 leading to SEQ ID NO:5.
Mohanta et al. teaches in the sample of thirteen watermelon verities the branch numbers varied from 4-6 (page 17, paragraph 2, page, page 176, table1). Therefore, it is not clear what modification in the watermelon genome would cause which level of increase in branch numbers.
Therefore, there is dearth of description of increased average number of secondary branches as compared to what control or standard (claims 1 and 4).
Kompella et al. (Published: 2017, Journal: ACS Synthetic Biology, 6(3): 446-454) teaches different premature stop codon wherein in some mutants of Fus3 as F13L and A30 does not have change to wildtype (page 450, table 1).
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The stop codon in DNA typically has one of the following sequences: TAG, TAA or TGA. However, since there is no effect on wild type, the watermelon plant would not have any difference compared to the wildtype watermelon plant. Instead, Applicant does not teach a mutant ClD14 gene carrying a premature stop codon in position 255 other than the amino acid exchange to STOP is at amino acid position of 155 of SEQ ID NO:2.
The existence of working examples:
The Specification or state of the art does not teach a person with skill in the art how to make and/or use the subject matter within the full scope of these claims because:
Applicant does not teach Applicant at least any one of the amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 would cause increase in number of secondary branches other than the homozygous W155Stop/ W155Stop of SEQ ID NO:2 leading to SEQ ID NO:5.
Lack of a working example is a critical factor to be considered, especially in a case involving an unpredictable and undeveloped art. See MPEP § 2164.
Genetech, 108 F.3d at 1366, states that “a patent is not a hunting license. It is not a reward for search, but compensation for its successful conclusion” and “[p]atent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable”.
In the absence of guidance from either the instant disclosure or the art, it would require undue trial and error experimentation for a skilled artisan to make and use the broadly claimed polynucleotide and polypeptides with missing or replaced, with no reasonable expectation of success in arriving at a protein variant having increase causing in a watermelon plant an increased average number of secondary branches when the mutant is in homozygous form.
Thus, in view of the unpredictability associated with the any amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 that would require to have the watermelon plant an increased average number of secondary branches when the mutant is in homozygous form, the lack of enabling guidance from either the instant disclosure or the art, and breath and diversity of the embodiments encompassed by the claimed genus, the lack of sufficient working examples, and the level of the art at the time of the invention, one of ordinary skill in the art must rely on undue trial and error experimentation to make and test the numerous polypeptides encompassed by the broad genera, in order to make and/or use the invention within the full scope of these claims.
For at least this reason, the Specification does not enable a person of skill in the art how to make and/or use the subject matter within the full scope of these claims.
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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 5-14 are rejected under 35 U.S.C. 103 as being unpatentable over is Lenini et al. (US Patent No.: US 7,314.979 B2, Date of Patent: Jan. 1, 2008), and further in view of Hu et al., and further in view of Ye et al. (Published Year: 2012, Journal: BMC bioinformatics, 13 : 1-11), and further in view of Paudel et al. (Published: 2019, Journal: Scientia Horticulturae 257 108665, https://doi.org/10.1016/j.scienta.2019.108665, pages 1-7) and as evidenced by Puglisi et al. (WIPO International Pub. No.: WO 2022/200149 A1, Pub. Date: 29 September 2022).
Claims are drawn to a method of detecting watermelon plant, a method of generating a PCR amplification product, a method of amplifying the genomic DNA of watermelon plant comprising ClD14 gene.
Regarding claim 5, Applicant discloses QTL mapping for secondary branching (also referred to as 'multi branching') was done on an F2 population developed by crossing the multi branching variety Sidekick F1 with a proprietary normal branching watem1elon plant (Response to Rejection, page 70, lines 1-3).
Applicant discloses it was found that a gene on chromosome 8 caused the multi branching phenotype in Sidekick F1 (page 70, line 7).
Applicant discloses the gene ClD14, contained a duplication of 24 nucleotides, which encoded 8 additional amino acids compared to the wild type gene, present in the normal-branching parent (page 70, lines 7-9). The extra amino acid from position 93-101 would have been missing amino acid in the wildtype claimed by claim 1 (see Figure 1 for alignment).
Applicant discloses the multibranching phenotype, as only seen when the mutant allele of the gene (comprising the 24-nudeotide duplication) was present in homozygous form (page 70, lines 9-11, Table in page 17).
Therefore, the mutant gene is found in Sidekick variety of watermelon. Puglisi et al. showed evidence that Sidekick is a watermelon variety taught by the US7314979B2 (i.e. by Laini et al.) which has the mutant allele for multibranching (page 4, lines 9-19). Laini et al. teaches the watermelon plant having an allele resulting in multibranching compact watermelon plant (Abstract).
Laini et al. teaches use of RFLP, PCR and SSR analysis for identifying the chromosomal location of their disclosed transgenic plant and selection and propagation of transformed plant and to determine common parentage using hybridizations, RFLP, PCR, SSR and sequencing (col. 15, lines 18-47). Laini et al. teaches single recessive dwarfing gene, dw-2 controls multibranching (col. 5, lines 11-21).
Hu et al. teaches enzyme-receptor DWARF14 (D14) regulates shoot branching (page 1, Abstract) wherein the mutation in D14 causes the increased branching in rice (see Figure 4).
Designing a specific primer is known in the art see. Ye teaches a tool Primer-BLAST which can be used to design new target-specific primers in one step as well as to check the specificity of pre-existing primers (Ye, page 1, Abstract). Ye et al. teaches their method can develop specific amplification of the desired target with the primers (Ye, page 1, Abstract). Ye teaches an example to design primers using the human zinc finger protein 419 (ZNF419) transcript variant 5 mRNA (Genbank accession: NM_001098494) (Ye, page 6, left paragraph 2).
Furthermore, Paudel et al. teaches using PCR primers for developing PCR amplification product (page3, left paragraph 1) in the F2 populations for identification of the desired gene in the F2 population (page4, right last paragraph).
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Someone skilled in the art before the effective date of filling of the invention from teaching suggestions from Laini et al. would sequence the watermelon plant Sidekick of Laini et al. to identify the D14 gene that would be associated with multibranching and would develop PCR primers for PCR products or select for D14 as taught by Ye et al. Such gene would have been identified using NCBI protein database for example the SEQ ID NO:2 had 99.1% identity to the Strigolactone esterase D14 of Cucumis melo (musk melon) such sequence would identify the D14 gene of watermelon by sequence similarity search from NCBI protein database search. Someone skilled in the art would obviously try-choosing from a finite number of identified D14 gene in the watermelon, do a genotyping assay based on nucleic acid hybridization making use of ClD14 allele to develop ClD14 specific primers or probes to identify ClD14 allele with any insertion, deletion and replacements. Furthermore, Paudel et al. teaches method of developing population and selecting population with desired gene in watermelon using PCR primers.
RESULT 2
A0A1S3BA45_CUCME
(NOTE: this sequence has 1 duplicate in the database searched)
ID A0A1S3BA45_CUCME Unreviewed; 267 AA.
AC A0A1S3BA45;
DT 12-APR-2017, integrated into UniProtKB/TrEMBL.
DT 12-APR-2017, sequence version 1.
DT 08-OCT-2025, entry version 39.
DE SubName: Full=Strigolactone esterase D14 {ECO:0000313|RefSeq:XP_008444562.1};
GN Name=LOC103487842 {ECO:0000313|RefSeq:XP_008444562.1};
GN Synonyms=103487842 {ECO:0000313|EnsemblPlants:MELO3C010810.2.1};
OS Cucumis melo (Muskmelon).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis.
OX NCBI_TaxID=3656 {ECO:0000313|Proteomes:UP001652600, ECO:0000313|RefSeq:XP_008444562.1};
RN [1] {ECO:0000313|EnsemblPlants:MELO3C010810.2.1}
RP IDENTIFICATION.
RG EnsemblPlants;
RL Submitted (MAR-2023) to UniProtKB.
RN [2] {ECO:0000313|RefSeq:XP_008444562.1}
RP IDENTIFICATION.
RG RefSeq;
RL Submitted (APR-2025) to UniProtKB.
CC -!- SIMILARITY: Belongs to the AB hydrolase superfamily.
CC {ECO:0000256|ARBA:ARBA00008645}.
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DR RefSeq; XP_008444562.1; XM_008446340.2.
DR EnsemblPlants; MELO3C010810.2.1; MELO3C010810.2.1; MELO3C010810.2.
DR GeneID; 103487842; -.
DR Gramene; MELO3C010810.2.1; MELO3C010810.2.1; MELO3C010810.2.
DR KEGG; cmo:103487842; -.
DR eggNOG; ENOG502QVRR; Eukaryota.
DR InParanoid; A0A1S3BA45; -.
DR OrthoDB; 408373at2759; -.
DR Proteomes; UP001652600; Chromosome 3.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR FunFam; 3.40.50.1820:FF:000042; probable strigolactone esterase DAD2; 1.
DR Gene3D; 3.40.50.1820; alpha/beta hydrolase; 1.
DR InterPro; IPR000073; AB_hydrolase_1.
DR InterPro; IPR029058; AB_hydrolase_fold.
DR PANTHER; PTHR43039; ESTERASE-RELATED; 1.
DR Pfam; PF12697; Abhydrolase_6; 1.
DR SUPFAM; SSF53474; alpha/beta-Hydrolases; 1.
PE 3: Inferred from homology;
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Reference proteome {ECO:0000313|Proteomes:UP001652600}.
FT DOMAIN 22..258
FT /note="AB hydrolase-1"
FT /evidence="ECO:0000259|Pfam:PF12697"
SQ SEQUENCE 267 AA; 29521 MW; 51D916CC4F4798D2 CRC64;
Query Match 99.1%; Score 1356; Length 267;
Best Local Similarity 98.5%;
Matches 263; Conservative 2; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MVNNALLEALNVRVLGTGDRSLVLAHGFGTDQSAWQLIYPSFTPYYRVILYDLVCAGSVN 60
|||||||||||||||||||| ||||||||||||||||:||||||||||||||||||||||
Db 1 MVNNALLEALNVRVLGTGDRFLVLAHGFGTDQSAWQLVYPSFTPYYRVILYDLVCAGSVN 60
Qy 61 PDFFDFSRYTTLDAFVDDLISILDSLHVHRCAFVGHSVSAMVGILASIRRPELFSKLILI 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PDFFDFSRYTTLDAFVDDLISILDSLHVHRCAFVGHSVSAMVGILASIRRPELFSKLILI 120
Qy 121 GASPRFLNDGDYHGGFEQSEIDRVFAAMKANYQSWVNGFAPLAVGADVPAAVQEFSRTLF 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GASPRFLNDGDYHGGFEQSEIDRVFAAMKANYQSWVNGFAPLAVGADVPAAVQEFSRTLF 180
Qy 181 NMRPDISLFVSKVIFSSDLRGVLGLVKVPCCIIQTAQDVSVPASVAIYLRDHLGGRNTVE 240
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||:|
Db 181 NMRPDISLFVSKVIFSSDLRGVLGLVKVPCCIIQTAQDVSVPTSVAIYLRDHLGGRNTIE 240
Qy 241 MLDTEGHLPHLSAPQLLVRKLRRALSR 267
|||||||||||||||||||||||||||
Db 241 MLDTEGHLPHLSAPQLLVRKLRRALSR 267
Regarding claims 6 and 9, the probe or the primer specific to ClD14 would have been at least 10 or at least 15 nucleotides long of SEQ ID NO:6 that encodes SEQ ID NO:2.
Regarding claims 7 and 8, the SEQ ID NO:5 is a genomic DNA encoding the mutant ClDl4Ins protein of SEQ ID NO: 1, comprising 24 nucleotides inserted/duplicated (Spec, page 68) which is found in Sidekick therefore the method would detect the SEQ ID NO:5 which would have codon change compared to the wildtype plant
Regarding claim 10, Ye et al. teaches developing forward and reverse primers (page1, abstract). Furthermore, Paudel et al. teaches developing KASP assays in watermelon.
Regarding claims 11 and 12, Ye et al. teaches their method can develop specific amplification of the desired target with the primers (Ye, page 1, Abstract).
Regarding claim 13, Paudel et al. teaches using PCR primers for developing PCR amplification product (page3, left paragraph 1) in the F2 populations for identification of the desired gene in the F2 population (page4, right last paragraph).
Regarding claim 14, The method would identify at least one or two copies of the wild type allele or mutant allele.
Conclusion
No claims are allowed.
Claims 1-4 appear free of prior art. The closest prior art is Lenini et al. (US Patent No.: US 7,314.979 B2, Date of Patent: Jan. 1, 2008). Lenini et al. teaches a watermelon plant and seed (claims 1-4) which have allele resulting in a multibranching compact watermelon plant (Abstract). The patentable distinction is Lenini et al. does not teach a plant having amino acid deletion or replacement in SEQ ID NO:2 starting at amino acid 22 and ending at amino acid 259 that causes the watermelon plant an increased average number of secondary branches when the mutant is in homozygous form.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663