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 .
Priority
Acknowledgment This present application is a U.S. National Stage Application of International Application No. PCT/EP2023/76581035047, filed 09/26/2023, which claims foreign priority from NETHERLANDS application 2033161 filed 09/27/2022.
The effective filing date is 09/27/2022.
Status of the Claims
Amendments dated 03/27/2025 are entered.
Claims 1-12 are pending and are examined herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 03/27/2025 is acknowledged and is being considered by the examiner.
Specification
The Specification is objected for the following informalities:
Lack of consistency with temperature recitations, for example “30 °C…30°C… 36 C” on page 4 lines 5-16.
The sentence bridging lines 29 and 30 on page 6 lacks clarity because it contains a double negative.
Claim Objections
Claim 1 is objected to because of the following informalities:
The first instance of a species within a claim set should spell out the full genus and species instead of an abbreviation of either, for example the S in “S. lycopersicum” on line 1 should be spelled out.
The acronym TBRFV is used without being defined or spelled out.
Use of semicolons where colons should be (e.g., line 3 after “of”, and line 10 after “defined as”.
Lack of consistency with the use of “an” or “a” preceding S. lycopersicum
Lack of consistency with italicization of S. lycopersicum.
Lack of “and” before the ultimate limitations or clauses in a list, for example there should be an “and” on line 8 after “position 571352,” and on line 13 or 14 after “that is resistant to TBRFV,” followed by “wherein the method further comprises….”
Claim 3 is objected to because of the following informalities:
Lack of consistency with italicization of S. lycopersicum.
Claims 11 is objected to because of the following informalities:
Line 2 should recite “from a plant obtainable from a method” instead of “from a plant or plant obtainable from a method”.
Appropriate correction is required.
Claim Interpretations
Regarding claims 1-12, the specification teaches is that “The aberrant phenotype locus (AP locus) is located on chromosome 9, originating from S. habrochaites. Furthermore, the AP locus can be co-inherited with a previously identified TBRFV resistance gene located on chromosome 8 in tomato and which shows segregation skewness in favor of the occurrence of the S. habrochaites allele (emphasis provided; page 3, lines 27-35).
Regarding claims 11-12, “a plant part, tissue, cell, and/or a seed” is being given the broadest reasonable interpretation of referring to components of a plant: a plant part, plant tissue, plant cell, and/or plant seed. Further, plant cells is being given the broadest reasonable interpretation of including plant embryos.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-12 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. All dependent claims are included in these rejections unless they contain a limitation that overcomes the deficiencies of the parent claim from which they depend. Details are listed below.
Claims 1-12 are rejected. Claims 1 and 5 recite:
“the AP locus is identified by the presence of one or more of an “T” on position 379858 in combination with a “C” on position 784380, preferably the presence of a “T” on position 428480 in combination with a “G” on position 601416, more preferably the presence of a “G” on position 474095 in combination with a “T” on position 571352.”
Regarding the phrase “One or more of an ‘T’ on position 379858 in combination with a ‘C’ on position 784380… 571352,” it is unclear whether applicant means one (“T”) or more (“TTT”) at position 379858 in combination with a ‘C’ on position 784380. Otherwise, it is unclear whether Applicant intends for the AP locus to be identified by the presence of a one or more combinations of SNPs (e.g., a “T” on position 379858 in combination with a “C” on position 784380, and/or a “T” on position 428480 in combination with a “G” on position 601416) or by the presence of one or more SNPs (e.g., “T” on position 379858, “C” on position 784380, ). The metes and bounds of the claim are unclear. Please clarify.
Claims 1-12 are further still rejected because the phrases "preferably" and “more preferably” recited in claim 1 render the claim(s) indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. Description of examples or preferences is properly set forth in the specification rather than the claims. If stated in the claims, examples and preferences lead to confusion over the intended scope of a claim. See MPEP § 2173.05(d). Similarly, claim 5 recites “preferably.” Limitations including the word “preferably” are not given any patentable weight.
Claims 1-4 and 11 are further rejected under 35 U.S.C. 112(b) because claim 1 lacks clarity. The preamble of Claim 1 recites “a method for selecting an S. lycopersicum plant that is tolerant to high temperature conditions [wherein the method comprises] selecting the S. lycopersicum plants that do not have the AP locus [as defined in lines 4-8 of claim 1].” The claim continues “wherein the method in addition provides a S. lycopersicum plant that is resistant to TBRFV” (emphasis provided). It is not clear if this additionally provided TBRFV-resistant plant is the same plant being selected for lack of the defined AP locus or is another individual plant.
Claims 1-4, 6-7, and 11 are further rejected because claims 1, 3, and 6-7 recite “at least [a number of] days” where temperature conditions are maintained. In a method for selecting an S. lycopersicum plant that is tolerant to high temperature conditions and in a plant that is tolerant to high temperature conditions it is important to distinctly indicate whether the total duration of high temperature conditions is a continuous or is the summed duration of separated high temperature conditions. In the Specification, applicant discloses that phenotype scoring occurred “3 weeks after sowing” (page 6, line 31). However, Applicant does not explicitly disclose how many days the sown seeds, or plants thereof, were left in the recited 36 °C during day and 30°C during night conditions. Thus, it is unclear what the scope of the claims are.
Claims 1-4, 6, and 11 are further rejected because claims 1 and 6 recite “agronomical phenotype.” This phrase is not defined in the disclosure. Merriam Webster defines agronomical as “of, relating to, or designed to promote agronomy” (https://www.merriam-webster.com/dictionary/agronomic). Characterization of a phenotype as agronomical is driven by geography, as a plant trait or phenotype only provides agricultural value or promotes agronomy within the specific climatic, soil, and management conditions of a target environment. This makes the characterization subjective and relative to socio-economic and local environmental parameters. It is unclear what an agronomical phenotype is because there are so many! Pollinator attracting exudates? Tall, short, viny, large fruit, deep roots? Fuzz-less, purple flesh, white seeds? Grown in which field?
Claims 1-4, 7, and 11 are further rejected. Claims 1 and 7 both recite the term “about” twice in relation to ranges of time durations: “5 to 7h” and “17-19h.” The term “about” is not defined in the Specification. Per MPEP § 2111.01 subpart IV(A), the plain and ordinary meaning of "about" is "approximately." In the instant application, an approximation of 10% per second would be 30 minutes for 5 hours and 1h42min for 17h. These are See MPEP § 2173.05(b) subpart III(A) and 2111.01 subpart IV(A). However, the Specification does recite more instances of about, exemplarily “these indicated temperatures should be maintained day and night, i.e. including the high temperature of at least 28°C, preferably at least 30°C at night for about 6 hours and preferably at least 36 C at daytime for about 18 hours, in order to trigger heat stress in the plant” (emphasis provided; Specification page 4 lines 5-11). It seems the ranges, “5 to 7h” and “17-19h,” are 1h approximations from 6 hours and 18 hours respectively. It is unclear if the ranges, “5 to 7h” and “17-19h,” are to undergo the same 1h approximation when preceded by “about?” Or less than 1h seeing as they are approximations? Or different approximations seeing as the ranges are so different from each other? And how do these ranges relate to the 24 hours that are allotted within a day? Applicant is advised to clarify without bringing in New Matter.
Claims 5, 8-10, and 12 are further rejected under 35 U.S.C. 112(b) because claim 5 lacks clarity. Claim 5 is an independent claim drawn to “an S. lycopersicum plant [of claim 5] that is tolerant to high temperature conditions.” The term “high” is a relative term. It is unclear which temperatures are considered high. Thus, the metes and bounds of the claim are unclear.
Claims 5, 7-10, and 12 are further rejected. Claim 5’s recitation of a S. lycopersicum plant that is tolerant to high temperature conditions, “wherein the plant is absent of an AP locus in chr 9 of its genome” (emphasis provided), which is a negative limitation. It is unclear from the claim language what effect the presence or absence of the AP locus in the plant’s genome is on the plant’s phenotype.
The specification teaches is that the AP locus is co-inherited from the S. habrochaites source, which was used as a donor plant providing TBFRV resistance to S. lycopersicum plants via introgression (Specification, page ,7 lines 20-25).
The plants in claim 5, though, are not limited to S. lycopersicum plants with S. habrochaites-sourced TBFRV resistance or introgressions. All other S. lycopersicum plants not introgressed with S. habrochaites appear to lack the AP locus such that the negative limitation (wherein, the plant is absent of an AP locus in chr 9 of its genome) is not very limiting.
Claim Rejections - 35 USC § 112(a)
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.
Written Description
Claims 1-12 rejected under 35 U.S.C. 112(a) 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.
Claim 1 is broadly directed to a method for selecting an S. lycopersicum plant that is tolerant to high temperature conditions, having an agronomical phenotype which comprises:
screening S. lycopersicum plants for the absence of an AP locus on chr 9, where in the presence of the AP locus is identified by the presence of one or more of an “T” on position 379858 in combination with a “C” on position 784380, preferably the presence of a “T” on position 428480 in combination with a “G” on position 601416, more preferably the presence of a “G” on position 474095 in combination with a “T” on position 571352,
selecting the S. lycopersicum plants that do not comprise an AP locus on chr 9 wherein said high temperature conditions is defined as: keeping said plant at a temperature of least 28° C. for at least 7 days, preferably for at least 14 days, preferably at least 30° C. at night for about 5 to 7 h, and at least above 36° C. at daytime for about 17 to 19 h,
wherein the method in addition provides a S. lycopersicum plant that is resistant to TBRFV, wherein the method further comprises the step of screening and selecting a plant that is resistant to Tobamovirus, wherein said selection comprises establishing the presence of a TBRFV resistance gene comprising a coding sequence having at least 90% nucleotide sequence identity with SEQ ID No. 1.
Claim 5 is drawn to a S. lycopersicum plant that is tolerant to high temperature conditions, wherein the plant is absent of an AP locus on chr 9 in its genome, wherein presence of the AP locus is identified by the presence of one or more of an “T” on position 379858 in combination with a “C” on position 784380, preferably the presence of a “T” on position 428480 in combination with a “G” on position 601416, more preferably the presence of a “G” on position 474095 in combination with a “T” on position 571352.
Claim 7 is drawn to the plant of claim 5 wherein “high temperature conditions are maintained for at least 14 days, and wherein the high temperature conditions are at least 30 °C at night for about 5 to 7 h and at least above 36 °C at daytime for about 17 to 19 h”
Regarding the AP locus and its absence, and high temperature conditions Applicant describes:
The aberrant phenotype locus (AP locus), identified as a genetic region or locus controlling physiological disorder triggered by heat stress in tomato, is located on chromosome 9, originating from S. habrochaites, can be co-inherited with a previously identified TBRFV resistance gene located on chromosome 8 in tomato, and is about 300 Kbp in size, comprising the 48 putative genes.
On the basis of specific SNPs, the absence or presence of AP was determined in view of the S. lycopersicum Heinz 4.0 genome (also known as SL4.0 genome) and S. habrochaites genome, chr 9.
Table 1, which shows the SNP positions and the specific SNP on that position used to determine if the AP locus was absent or present based on the S. lycopersicum Heinz 4.0 genome (see snippet below).
Table 1
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274
875
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Greyscale
when on position 379858 an “T” and on position 784380 a “C” was present on chr 9, the plant comprised the AP locus and showed the aberrant phenotype. More preferably in case a “G” was present on position 474095 in combination with a “T” present on position 571352 on chr 9, the plant comprised the AP locus and showed the aberrant phenotype.
tomato plants (S. lycopersicum) tested to be resistant to TBRFV and comprise the TBRFV resistance gene, as previously described in WO2020147921, and wherein grown at heat stress conditions (>30° C.) in a greenhouse, plants that are comprised of the AP locus homozygous in their genomes, show the aberrant phenotype while plants that do not comprise the AP locus do not show the aberrant phenotype (Fig. 1 Caption).
Seeds of the mapping population were sown in soil trays and placed in a growing chamber at the conditions: 18 hours of light (day)/ 6 hours of darkness (night); with 36°C during day conditions, and 30°C during night conditions.
Regarding the AP locus and its absence Applicant does not describe:
The SNP positions for all S. lycopersicum plants, just in view of the S. lycopersicum Heinz.
The contiguous sequence context of the SNPs.
The aberrant phenotype locus (AP locus), identified as a genetic region or locus controlling physiological disorder triggered by heat stress in tomato, being identifiable by the presence of one SNP.
Growing plants at least above 36 °C at daytime and at above 30 °C at night for more than 3 weeks (i.e., 21 days)
Applicant has reduced to practice SNPs with position numbers claimed relative to a designated chromosome 9 of a, at least, fourth version of the genome of a particular cultivar, S. lycopersicum Heinz, as indicators of the presence of an about 300 Kbp region, yet claims the entire S. lycopersicum species or selection from the entire species.
Applicant has not described the data or SNPs and positions indicative of the presence of the AP locus relative to a fixed sequence represented by a SEQ ID NO and disclosed in the Sequence Listing. It is known in the art that sequence variation exists between cultivars and generations, and even within generations such that the positions of coding region along a chromosome vary much less individual nucleotides or pair which are subject to transitions and transversions, and insertions and deletions. Genes located between positions 379858 and 784380 on chromosome 9 could be located on positions 379860 and 784382 on chromosome 9 of another plant in the same species.
Though not in the claims, it is noted that Applicant does disclose the S. lycopersicum Heinz 4.0 genome in the Specification and that the absence or presence of AP, originating from S. habrochaites, was determined in view of specific SNPs between the S. lycopersicum Heinz 4.0 genome (also known as SL4.0 genome) and S. habrochaites was basis of the genome, chr 9 (page 3, lines 27-35; page 7, lines 27-29. However, Su (Su, X., Wang, B., Geng, X. et al. A high-continuity and annotated tomato reference genome. BMC Genomics 22, 898 (2021). https://doi.org/10.1186/s12864-021-08212-x) teaches that “[a]fter several updates of tomato genome, the SL4.0 tomato genome[, used by applicant,] has reached chromosomal assembly, but its continuity and integrity remains to be further improved to facilitate the identification of large structural variations and gene mining” (background, para 2). This suggests that the continuity of chromosome assemblies, including that chromosome 9, in SL4.0 are potentially without integrity and are subject to change including the reordering of chromosomal regions which would disrupt numbering. This is such that the SNPs recited in claims 1 and 5 are without the context of the surrounding sequences within which the SNPs are to be screened for so long as a fixed sequence is absent. The identification of the instantly claimed SNPs is thus unclear.
Applicant has reduced to practice identifying the presence of the AP locus, originating from S. habrochaites, using a combination of at least two SNPS ranging from 97257 to 404,522 nucleotides apart, yet is claiming identifying the presence of the AP locus, originating from S. habrochaites, using “one or more” SNPs (Specification, paragraph bridging pages 7 and 8; claims 1 and 5). It is not clear from the specification that the presence of only one or two of recited SNPs correlates with tolerance to “high temperature conditions” as defined by claims 1, 6, and 7.
Applicant has reduced to practice sowing seeds in soil trays and placing them in a growing chamber at the conditions: 18 hours of light (day)/ 6 hours of darkness (night); with 36°C during day conditions, and 30°C during night conditions. Although, Applicant does not explicitly disclose how many days the sown seeds, or plants thereof, were left in the recited 36 °C during day and 30°C during night conditions, applicant discloses Phenotype scoring “3 weeks after sowing” (page 6, line 31). Yet applicant claims, in claim 7, conditions that include temperatures above the 36 °C during day and 30 °C during night conditions that were reduced to practice. The recitation of “at least 28 °C” in claims 1, 3, and 6 also includes temperatures above the 36 °C during day and 30 °C during night conditions that were reduced to practice. The duration of the high temperature conditions being at least 7 days ( claims 1, 3 and 6) and 14 days ( claim 7) includes more days than are in “3 weeks” (page 6, line 31).
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 5-7, 11, and 12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claims do not fall within at least one of the four categories of patent eligible subject matter because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon including products of nature, or an abstract idea) without significantly more. All dependent claims are included in these rejections unless they contain a limitation that overcomes the deficiencies of the parent claim from which they depend. The rationale for this determination is explained below.
Claims 5-7, and 12 are rejected because of claim 5’s recitation of a S. lycopersicum plant, “wherein the plant is absent of an AP locus in chr 9 of its genome” (emphasis provided). The specification teaches is that the AP locus is co-inherited from the S. habrochaites source, which was used as a donor plant, during introgression of the TBFRV resistance gene into S. lycopersicum plants (Specification, page ,7 lines 20-25).
The plants in claim 5, though, are not limited to S. lycopersicum plants with S. habrochaites-sourced TBFRV resistance or introgressions. All other S. lycopersicum plants not introgressed with S. habrochaites appear to lack the AP locus such that the negative limitation (wherein, the plant is absent of an AP locus in chr 9 of its genome) is not very limiting and includes naturally occurring S. lycopersicum plants.
Claim 11 is rejected and claim 12 is further rejected under 35 U.S.C. 101. Claim 11 depends from claim 1 and recite(s) a cell and/or seed of a plant obtainable by the method of claim 1. Claim 12 depends from claim 5 and recite(s) a cell and/or seed of a S. lycopersicum plant absent of an AP locus on chr 9 of its genome.
These judicial exceptions are not integrated into a practical application because an embryo cell and a seed of a plant may only comprise half of the genes of the parent plant due to Mendelian genetics. These compositions will naturally lack the instantly claimed AP locus and may also lack the TBRFV resistance gene encoding gene shown in SEQ ID NO: 1. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims do not require that the seed comprises the TBRFV resistance gene encoding gene shown in SEQ ID NO: 1. Amendment of the claim to recite that the seed comprises said gene would overcome the rejection.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 5-6 and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Karkute (Karkute, S.G., Ansari, W.A., Singh, A.K. et al. Characterization of high-temperature stress-tolerant tomato (Solanum lycopersicum L.) genotypes by biochemical analysis and expression profiling of heat-responsive genes. 3 Biotech 11, 45 (2021). https://doi.org/10.1007/s13205-020-02587-6, published January 1st, 2021, Cited in IDS).
The specification teaches is that “The aberrant phenotype locus (AP locus) is located on chromosome 9, originating from S. habrochaites. Furthermore, the AP locus can be co-inherited with a previously identified TBRFV resistance gene located on chromosome 8 in tomato and which shows segregation skewness in favor of the occurrence of the S. habrochaites allele”(emphasis provided; page 3, lines 27-35).
Karkute teaches “high‑temperature stress‑tolerant tomato (Solanum lycopersicum L.)” which were not introgressed with S. habrochaites meaning they do not comprise the entirety of the AP locus, absent evidence to the contrary (Title, entire paper). This reads on claim 5.
Accordingly, the claimed invention is anticipated by, or in the alternative, is obvious in view of the prior art. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of the prior art, the burden of proof is upon the Applicant to show an unobvious distinction between the claimed plant and the plant of the prior art. See In re Best, 562F.2d 1252, 195 USPQ 430 (CCPA 1977).
Regarding claim 6, Karkute teaches that “ high-temperature stress-tolerant tomato genotypes H88-78-1 and CLN-1621…were germinated and grown in a greenhouse at 25 ± 2 °C [and that] Plants were exposed to high-temperature stress at 42 °C by transferring them to a growth chamber after 25 days of transplanting.” Here, Karkute teaches 25 ± 2 °C, (i.e., 27 °C) for 25 days (i.e., more than 7 days) such that without a distinct criticality of the 1°C or 3.57% difference, this is the claimed invention is anticipated by, or in the alternative, is obvious in view of the prior art. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of the prior art, the burden of proof is upon the Applicant to show an unobvious distinction between the claimed plant and the plant of the prior art. See In re Best, 562F.2d 1252, 195 USPQ 430 (CCPA 1977).
Regarding claim 12, Karkute teaches “seeds of high-temperature stress-tolerant tomato genotypes…were germinated and grown [i.e., plants with leaves]…and leaf samples were collected [i.e., plant part, tissue, cells] ” (c.f., claim 12) (page 2, col 2, first full para).
Thus, Karkute anticipates the claimed inventions.
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.
Claims 1-6 and 8-12 are rejected under 35 U.S.C. 103 as being unpatentable over Ykema (U.S. Patent Application Publication No. 20210238627A1, assigned to Enza Zaden Beheer BV, titled ‘Tomato plant resistant to tomato brown rugose fruit virus’, published August 5th, 2021) in view of Karkute (Karkute, S.G., Ansari, W.A., Singh, A.K. et al. Characterization of high-temperature stress-tolerant tomato (Solanum lycopersicum L.) genotypes by biochemical analysis and expression profiling of heat-responsive genes. 3 Biotech 11, 45 (2021). https://doi.org/10.1007/s13205-020-02587-6, published January 1st, 2021, Cited in IDS).
Ykema teaches “a Tobamovirus resistant Solanum lycopersicum plant, wherein the plant comprises a Tomato Brown Rugose Fruit Virus (TBRFV) resistance gene encoding a TBRFV resistance protein comprising polypeptide sequence SEQ ID NO: 116 and wherein the resistance gene comprises nucleotide sequence SEQ ID NO: 115” (Ykema claims 1-2).
Ykema’s SEQ ID NOs: 115 and 116 show 100% identity to present SEQ ID NOs: 1 and 2 respectively with no mismatches, or gaps (data not shown)(c.f., claims 1, 4 and 8-9).
Ykema also teaches “a method for providing a plant of the S. lycopersicum species that is resistant to Tobamovirus,” (para 033) where “plants… were screened for resistance by inoculation with TBRFV” (c.f., claim 10)(emphasis provided; para 0043), “Tomato plants comprising the TBRFV resistance locus [were] selected” (para 0066) “wherein said selection comprises establishing the presence of the resistance gene genomic sequence or resistance locus of present invention” (para 0033) and that the resistance locus is “the TBRFV resistance gene of SEQ ID No. 115” (para 0071).
Ykema’s above teachings read on claims 4 and 8-10 and the partial recitation of claim 1 below:
wherein the method in addition provides a S. lycopersicum plant that is resistant to TBRFV, wherein the method further comprises the step of screening and selecting a plant that is resistant to Tobamovirus, wherein said selection comprises establishing the presence of a TBRFV resistance gene comprising a coding sequence having at least 90% nucleotide sequence identity with SEQ ID No. 1.;
Ykema additionally teaches that “transferring the identified [resistance] genomic sequence[, nucleotide sequence SEQ ID NO: 115,] into a S. lycopersicum plant thereby conferring Tobamovirus resistance to said S. lycopersicum plant (para 0035).
Ykema further teaches that the “transferring can be done by crossing the selected [TBRFV resistant] S. habrochaites plant with a S. lycopersicum [and that] subsequently, a Tobamovirus resistant S. lycopersicum plant can be selected by Inoculation with TBRFV” (para 0064).
Regarding crossing, Ykema also teaches “further backcrosses” starting with backcrossing of “F1 plants created with LYC4943 plant 3 (90479-3) [and] selected for resistance phenotype [with] S. lycopersicum lines OT9 and OT1317 as backcross lines [wherein neither had previously been introgressed with S. habrochaites so would not comprise the AP locus, absent evidence to the contrary. ]” (para 0052). Backcrossing is well-known in the art and enables transfer of a desired trait (i.e., comprising SEQ ID NO: 115) from a donor plant/variety (i.e., F1 plants created with LYC4943 plant 3) into the favored genetic background of another variety, termed recurrent parent (i.e., S. lycopersicum lines OT9 and OT1317).
So, although Ykema does not explicitly teach the one or more SNP positions recited in the instant claims, having identified SEQ ID NO: 115 as the locus or gene of interest, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to backcross TBRFV resistant S. lycopersicum plants produced with S. habrochaites LYC4943 plant 3 and comprising SEQ ID NO: 115 with S. lycopersicum plants of known/desirable genetic backgrounds where the method of doing would include screening and selecting S. lycopersicum plants that do not comprise the AP locus. One would have been motivated to do this in order to combine the TBRFV resistant gene with the traits of the plants of known/desirable genetic background because linkage drag and skewed segregation are known in the art.
Ykema does not explicitly teach the definition of high temperature conditions as recited in claim 1: “keeping said plant at a temperature of least 28 °C for at least 7 days.”
The specification discloses is that “The aberrant phenotype locus (AP locus) is located on chromosome 9, originating from S. habrochaites. Furthermore, the AP locus can be co-inherited with a previously identified TBRFV resistance gene located on chromosome 8 in tomato and which shows segregation skewness in favor of the occurrence of the S. habrochaites allele” (emphasis provided; page 3, lines 27-35).
Karkute teaches “high‑temperature stress‑tolerant tomato (Solanum lycopersicum L.)” which were not introgressed with S. habrochaites meaning they do not comprise the entirety of the AP locus, absent evidence to the contrary (Title, entire paper). This reads on claim 5 and since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of the prior art, the burden of proof is upon the Applicant to show an unobvious distinction between the claimed plant and the plant of the prior art. See In re Best, 562F.2d 1252, 195 USPQ 430 (CCPA 1977).
Karkute also teaches that “ high-temperature stress-tolerant tomato genotypes H88-78-1 and CLN-1621…were germinated and grown in a greenhouse at 25 ± 2 °C [and that] Plants were exposed to high-temperature stress at 42 °C by transferring them to a growth chamber after 25 days of transplanting.” Here, Karkute teaches 25 ± 2 °C, (i.e., 27 °C) for 25 days (i.e., more than 7 days) such that without a distinct criticality of the 1°C or 3.57% difference, this is obvious over Applicants definition of high temperature conditions recited in claim 1 and again in claims 3 and 6.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the SEQ ID NO: 115, the introgressing with S. habrochaites, the backcrossing, and the screening for resistance by inoculation with TBRFV teachings of Ykema with the “high‑temperature stress‑tolerant tomato (Solanum lycopersicum L.)” plants of Karkute, crossing Karkute’s plants with S. habrochaites then backcrossing the SEQ ID NO: 115 bearing progeny of the cross with Karkute’s plants, thus, arriving upon the claimed method of claim 1 and the claimed plant of claim 5. One would have been motivated to do this in order to combine the TBRFV resistant gene with the high‑temperature stress‑tolerant tomato traits of the plants of known/desirable genetic background because “it is extremely important to improve the high-temperature stress tolerance of crops through molecular manipulations” (Karkute, introduction para), “ there is a need in the art for…TBRFV resistant S. lycopersicum” (Ykema, para 0010), and linkage drag and skewed segregation are known in the art.
Regarding claim 2-3 and 6, although Karkute did not compare their high-temperature stress-tolerant tomato plants to plants that were identified as having an AP locus, Karkute’s high-temperature stress-tolerant tomato plants do show high-temperature stress tolerance and do not have an AP Locus, absent evidence to the contrary. Accordingly, the claimed invention is obvious in view of the prior art. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of the prior art, the burden of proof is upon the Applicant to show an unobvious distinction between the claimed plant and the plant of the prior art. See In re Best, 562F.2d 1252, 195 USPQ 430 (CCPA 1977).
Regarding claims 11-12, Ykema teaches backcrossing which includes production of plants and seeds from the plant of the invention.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Ykema and Karkute as applied above to claims 1-6 and 8-12 in view of Scarano (Scarano A, et al. Selection of tomato landraces with high fruit yield and nutritional quality under elevated temperatures. J Sci Food Agric. 2020 Apr;100(6):2791-2799. doi: 10.1002/jsfa.10312. Epub 2020 Feb 29. PMID: 32022274; PMCID: PMC7187367., published 2020), Ro (Ro S, et al. Response of Tomato Genotypes under Different High Temperatures in Field and Greenhouse Conditions. Plants (Basel). 2021 Feb 27;10(3):449. doi: 10.3390/plants10030449. PMID: 33673537; PMCID: PMC7997173., published 2021), Sangu (Sangu E, et al. Expression of genes for the biosynthesis of compatible solutes during pollen development under heat stress in tomato (Solanum lycopersicum). J Plant Physiol. 2015 Apr 15;178:10-6. doi: 10.1016/j.jplph.2015.02.002. Epub 2015 Feb 20. PMID: 25747289., published 2015) and Rajametov ( Rajametov, S.N.; et al. Heat Treatment in Two Tomato Cultivars: A Study of the Effect on Physiological and Growth Recovery. Horticulturae 2021, 7, 119. https://doi.org/10.3390/horticulturae7050119, published May 21st, 2021).
Ykema and Karkute do not explicitly teach that high temperature conditions are maintained for at least 14 days, and wherein the high temperature conditions are at least 30 °C at night for about 5 to 7h and at least above 36 °C at daytime for about 17 to 19h.
In the abstract Scarano teaches of “extreme or adverse events induced by climatic fluctuations as important threat[s] for plants growth and agricultural production… [and that] the identification of genotypes that are good yield performer at high temperatures is becoming increasingly necessary for future breeding programs.”
Scarano also teaches that when “A group of tomato landraces previously selected for yield performances under high temperatures in two regions of southern Italy, Campania and Apulia, in 2016… [were tested] again under high temperatures in an open field in the Apulia region in 2017…,” “more than 40 days (38.5% of the whole growing season, from the end of May to the beginning of September) reached temperatures over 32 °C, which is considered the critical temperature affecting the reproductive stage of tomato, as well as of other species[;] On 16 days (15.4%), a temperature higher than 35° C was even recorded [and that] in addition, very high temperatures were also recorded in the night, and this is considered a critical point for pollen maturation” (results and discussion, para 1). In the conclusion Scarano teaches that after testing, “one landrace (PDVIT) was selected as a good compromise between yield performances and good fruit quality and nutritional traits when growing under high temperature”
This explicitly reads on the “ high temperature conditions are maintained for at least 14 days” limitation recited in claim 7.
However, although Scarano teaches of temperatures higher than 35 °C (i.e., at least above 36 °C at daytime), Scarano does not explicitly teach the duration as being “for about 17 to 19 h”.
Also, Scarano teaches of very high temperatures recorded in the night, but does not explicitly teach high temperature conditions at least 30° C at night “for about 5 to 7 h.”
Ro teaches that “CLN1621L was superior under high temperature conditions as the genotype could maintain high fruit settings… [corroborating] Sangu[‘s]… report that temperatures up to 35/28 °C day/night did not affect flower development of genotype CLN1621L and [CLN1621L] had higher fruit set as observed in [Ro’s] study” (emphasis provided; para bridging page 7 and 8). See the below snippet of Figure 4c showing the “temperature during the whole crop cycle of high temperature greenhouse conditions… [wherein] the solid line is a critical temperature at 33 °C for tomato production” (figure 4c caption) and where highs exceed 36 °C for consecutive weeks (i.e., at least 14 days).
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Sangu teaches that “Tomato (Solanum lycopersicum) … grows under diverse environmental conditions worldwide with optimal temperatures of 25–30 °C day and 20 °C night” (introduction, para 4). Sangu also teaches that “Kigamboni (KGMN) [in Tanzania] maintained average monthly temperatures of above 33 °C day and 27 °C night with a daily range of 28–43 °C/25–38 °C day/night throughout the hot season, therefore qualifying for screening the genotypes for heat stress tolerance (hot season)” (experimental design, para 2) and “heat stress tolerant CLN 1621L exhibited the highest fruit set” (page 13, para bridging columns), “exhibited relatively low cell membrane damage across 36 °C and 41 °C temperature treatment” (page 12, col 2, last para).
Rajametov teaches that “[tomato] seedlings were maintained under severe HT conditions (40 °C day/night, 16/8-h light/dark cycle) [i.e., at least 30 0°C at night for about 5 to 7 h and at least above 36 °C at daytime for about 17 to 19 h.] and light intensity of 800 µmol m−2 s−1 within 70% relative humidity… in the growth chamber for 7 days” (Materials and Methods para 1) and that in “heat-tolerant cultivar ‘Minichal’, fruit weight (3.6%) and fruit hardness (8.3%) were increased” (Abstract).
Although, neither Scarano, Ro, Sangu, nor Rajametov explicitly teach at least 30 °C at night for about 5 to 7h and at least above 36 °C at daytime for about 17 to 19h for at least 14 days, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Ykema and Karkute with Scarano, Ro, Sangu, or Rajametov because all teach a heat tolerant tomato cultivars after varying high temperature conditions including some well above 36 °C during the day and 30 °C at night. Absent evidence to the contrary, none of the heat tolerant tomato Solanum lycopersicum cultivars disclosed by either Scarano, Ro, Sangu, or Rajametov were introgressed with S. habrochaites meaning they do not comprise the entirety of the AP locus.
Without a distinct criticality of the duration of applicants defined high temperature conditions in comparison to those of Sangu, and especially Rajametov, the claimed invention is obvious in view of the cited prior art, and the state of the art in general. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of the prior art, the burden of proof is upon the Applicant to show an unobvious distinction between the claimed plant and the plant of the prior art. See In re Best, 562F.2d 1252, 195 USPQ 430 (CCPA 1977). One would have been motivated to ascertain such a heat tolerant plant because “the scenario of global environmental changes suggests a future increase…in the frequency of extreme temperatures in many areas of the world” (Karkute, introduction para).
Conclusion
No claims allowed.
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/YVETTE B. TAMUKONG/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
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