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 .
Status of Claims
Claims 1-2 are under examination on the merits.
Claims 5-10 and 13-16 are withdrawn from consideration.
The objections to claims 1-4 & 11-12 are withdrawn in light of Applicant’s amendments or cancelation of the claims.
The rejection of claims 1-4 & 11-12 under 35 U.S.C. 101 is withdrawn in light of Applicant’s amendments or cancelation of the claims.
The rejection of claims 4 & 11-12 under 35 U.S.C. 101 is withdrawn in light of Applicant’s cancelation of the claims.
The rejection of claims 2-3 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, is withdrawn in light of Applicant’s amendments or cancelation of the claims.
Claim Rejections - 35 USC § 112
Indefiniteness
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 2 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, 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.
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection set forth in the Office action mailed 7/8/2025, as applied to claims 2-4 & 11-12. Applicant' s arguments filed 9/29/20205 have been fully considered but they are not persuasive.
Claim 2 requires a KASP-10.6, KASP-29.9, KASP-5.1 and/or KASP-42.3 primer pair and that the introgression segment test positive for KASP-10.6 and KASP29.9 and negative for KASP-5.1 and/or KASP-42.3. The instant specification provides sequences for these primer pairs in table 1. Each primer “pair” comprises 3 distinct sequences. A person of ordinary skill in the art would understand a primer pair to comprise a forward and a reverse primer (two sequences, not three). A person of ordinary skill in the art would also read a nucleotide sequence in the 5’ to 3’ direction. One of skill in the art would understand the primers designated “F” and “H” in table 1 for each primer pair to differ in sequence at multiple positions, including at the 3’ end which is critical for primer specificity. Thus, the primer “pairs” of claim 2 presented in table 1 present distinct combinations of primers that would amplify different sequences in a genome.
If all three primers of each pair present in table 1 are intended to be used as a primer pair, more than one combination of each primer pair could potentially amplify depending on the genotype of the introgression. In other words, it is possible that both combinations for each primer pair could amplify (eg primers F and CR AND primers H and CR), just one combination could amplify, or no combinations could amplify. If a positive test result is specific to the primer combination that amplifies, neither claim 2 nor the specification provides clarification as to which combination constitutes the “positive” test result and which would be “negative”.
Claim 2 (lines 7-9) describes what a negative or positive test result would indicate with regard to the introgression segment but do not define what amplification results are needed for a result to be considered positive or negative. Because the primer “pairs” have more than 2 primer sequences and could lead to more than two possible results, and because the claim and the specification do not define which of the multiple results are to be considered negative and which are positive, claim 2 is indefinite.
Claim 2 is also indefinite in claiming both a plant (a product) and limitations that read on steps (a method). Lines 7-9 require that gene sequences corresponding to the primer pairs are “to be deleted” or “to be retained” based on the test result of the primer pairs. Deleting or retaining the sequences read on steps in a process. When a claim mixes statutory classes, it is unclear when direct infringement occurs. See MPEP 2173.05(p) II. If these limitations are not intended to be read as steps, it is unclear how they are intended to be interpreted, making the claim indefinite.
Applicant urges that the primer pairs in claim 2 and table 1 comprise 3 distinct sequences, two of which are allele-specific forward primers and one is a common reverse primer. Applicant urges that three primers are standard for KASP assays used in a single reaction and so “tested as positive” would be clear and definite to one of skill in the art (Remarks, page 13, paragraph 5 - page 14, paragraph 1).
This argument is unpersuasive, because claim 2 and the instant specification still do not define which primer combination would, upon amplification, provide positive test results that would indicate the presence of the gene sequences. Each of the forward primers in a 3-primer pair present allele-specific sequences that could be considered retained or deleted based on the amplification observed.
Written Description
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 1-2 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.
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection set forth in the Office action mailed 7/8/2025, as applied to claims 1-4 & 11-12. Applicant' s arguments filed 9/29/20205 have been fully considered but they are not persuasive.
Claims 1-2 are drawn to a N. tabacum plant with a Pseudomonas syringae pv. tabaci-resistant short WZ introgression segment reduced by a drag gene component of at least 500Kb wherein the drag gene component comprises the sequence shown in SEQ ID NO: 1 and/or 2 and a gene segment adjacent to the sequence. Claim 2 further requires that the introgression segment tests positive for a KASP-10.6 primer pair and a KASP-29.9 primer pair and negative for a KASP-5.1 primer pair and/or a KASP-42.3 primer pair. The instant specification defines a “short WZ introgression segment” as a DNA segment obtained by partially or completely deleting a non-target gene component and retaining disease resistance (paragraph [0026]) and a “drag gene component” as a gene component on the WZ introgression segment that includes a drag gene but does not have resistance for a target disease (paragraph [0027]).
Thus, claim 1 broadly requires a plant with an introgression segment, which reads on a nucleic acid molecule, comprising at least part of the sequence of the WZ introgression with resistance to Pseudomonas syringae pv. tabaci, and claim 2 requires that the nucleic acid molecule be able to test positive for a KASP-10.6 and KASP-29.9 primer pair.
The instant specification has described one long WZ introgression from the resistant T6 genotype (paragraph [0054]), with an introgression believed to be 65Mb long (paragraph [0006]). The instant specification has further described nine short WZ introgressions (table 2), of which 4 are resistant (table 3). The instant specification provides KASP-5.1, KASP-10.6, KASP-29.9, and KASP-42.3 primer pairs to determine WZ identity across the region of the introgression (table 1, table 3). The specification teaches sequences (SEQ ID NO: 1 & 2) flanking KASP-5.1 and KASP-42.3 for 500Kb on each side (paragraph [0081]).
The claims require that the plant comprise an introgression that is reduced by a 500Kb component comprising the sequence of SEQ ID NO: 1 and/or 2 and an adjacent gene segment. Since both SEQ ID NO: 1 & 2 are longer than 500Kb, this description of a short WZ introgression encompasses nucleic acid molecules that are truncated on either or both ends of the long WZ introgression segment. Examples of a representative sample of such segments that are resistant to Pseudomonas syringae pv. tabaci are not provided by the instant specification. The instant specification does not describe the structural feature(s) of the WZ introgression responsible for resistance to Pseudomonas syringae pv. tabaci.
The WZ introgression was known in the art prior to the effective filing date of the instant application (Shi et al (2019) Mol. Breeding. 39: 102 (published 6/28/2019, hereafter Shi), page 1, right column, paragraph 2-page 2, left column, paragraph 1). Recombination of the WZ introgression segment was also described in the art (Woodend et al (1992) Euphytica. 64: 149-156, hereafter Woodend, page 155, left column, paragraph 2) although the potential for recombination was described as low (Shi, page 8, left column, paragraph 2 & page 6, right column, paragraph 2). The genetic elements responsible for resistance to Pseudomonas syringae pv. tabaci are not described in the art.
Because the instant specification does not provide the structural features that distinguish a short WZ introgression segment with Pseudomonas syringae pv. tabaci resistance and has not described examples of such short WZ introgression segment across the full scope of the claimed introgression segments, one of ordinary skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the disclosed species.
Hence, Applicant has not, in fact, described N. tabacum plants with Pseudomonas syringae pv. tabaci-resistant short WZ introgression segments over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Applicant urges that the specification describes multiple short WZ introgression segments and characterizes several resistant lines and are functionally resistant to Pseudomonas syringae pv. tabaci which are representative species within the claimed genus. Applicant urges that written description is satisfied by a sufficient number of representative species of a genus when the function and structure are correlated (Remarks, page 16, paragraph 2). Applicant urges that the claims are directed to an introgression segment with a defined positive marker region between KASP-10.6 and KASP-29.9 and negative marker region around SEQ ID NOs: 1 & 2 to form a functionally defined structure to identify the introgression. Applicant urges that the structure of the positive marker region and negative marker regions demonstrate possession of the claimed genus of resistant plants within the claims (Remarks page 16, paragraph 3).
This argument is unpersuasive. First, claim 1 does not require a defined positive marker region responsible for the resistance. The negative limitations of claim 1 do not positively require any structural feature responsible for the resistance. As there is no definite structure correlated with the required function, the six resistant plants described in the specification (two of which comprise markers for a full length WZ introgression, table 3) cannot be considered representative of the full scope of the claimed genus.
Second, even with the additional positive limitation of markers in claim 2, the specification (table 3) only describes 6 plants with resistance, one of which comprises the full length WZ introgression (T6) and one of which is heterozygous for the full length WZ introgression across all markers (R0). So, Applicant has provided only 4 plants that may be considered examples of resistant plants with a short WZ introgression segment that do not also have a full length WZ introgression segment.
The resistant plants described in table 3 are described as to the genotype at each primer pair. Claims 1-2, however, require a segment reduced by SEQ ID NO: 1 and/or SEQ ID NO: 2. Both of these sequences are 1,000,000bp long and flank on both sides either KASP-5.1 or KASP-42.3 (paragraph [0081]). The absence of a long WZ genotype at KASP-5.1 (seen in 3 of the resistant plants of table 3) does not necessarily indicate the absence of the full 1,000,000bp long SEQ ID NO: 1 in resistant plants, although this is required by claim 1. More critically, there are 5.5Mb between KASP-5.1 and KASP-10.6 and 12.4Mb between KASP-29.9 and KASP-42.3 (Shi table S1). The genus of short introgression segments lacking the 1,000,000bp long SEQ ID NO: 1 or 1,000,000bp long SEQ ID NO: 2 and comprising positive results for markers KASP-10.6 and KASP-29.9 encompasses segments that can vary in length by 5Mb on one end or nearly 12Mb on the other. The single resistant plant example in the specification that is negative for KASP-42.3 and positive for KASP-29.9 (49-12B) cannot be considered a representative sample for recombination events over this 12Mb region. Conceivably, the locus providing resistance could be found outside the region delimited by KASP-10.6 and KASP-29.9, since the instant specification does not provide examples of recombination across the full scope of these regions and does not describe the specific genetic feature responsible for resistance.
Given the very long segment of DNA encompassed by the introgression, the relatively few recombinant short introgression resistant plants recovered, and the lack of description of the feature(s) responsible for resistance within the large DNA segment negatively recited, one of ordinary skill in the art would not have recognized that Applicant was in possession of the full genus of resistant plants given the few examples and markers provided.
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.
Claims 1-2 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Shi et al (2019) Mol. Breeding. 39: 102 (published 6/28/2019, hereafter Shi, uploaded along with table S1) taken with the evidence of Woodend et al (1992) Euphytica. 64: 149-156 (hereafter Woodend).
Due to Applicant' s amendment of the claims, the rejection is modified from the rejection set forth in the Office action mailed 7/8/2025, as applied to claims 1-4 & 11-12. Applicant' s arguments filed 9/29/2025 have been fully considered but they are not persuasive.
Claim 1 is drawn to an N. tabacum plant with a Pseudomonas syringae pv. tabaci-resistant short WZ introgression segment reduced by a drag gene component of at least 500Kb comprising the sequence shown in SEQ ID NO: 1 and/or 2 and an adjacent gene segment and a gene segment adjacent, tested as positive for a KASP-10.6 primer pair and a KASP-29.9 primer pair and negative for a KASP-5.1 primer pair and/or a KASP-42.3 primer pair.
It is not definite what “tested as positive” and “tested as negative” means with regard to the primer pairs comprising 3 primers in claim 2, but for the purpose of examination here positive has been interpreted to mean at least one of the possible combinations of the 3 primers listed for each pair amplifies a PCR product and negative has been interpreted to mean no combinations of the 3 primers successfully amplifies a PCR product.
The instant specification defines a short WZ introgression segment as a DNA segment obtained by partially or completely deleting a non-target gene component linked to disease resistance on the WZ introgression segment and retaining disease resistance (paragraph [0026]). The full length WZ introgression segment comprises segments that could be considered short WZ introgression segments by Applicant’s definition. The method of obtaining a product, such as a DNA segment, does not carry patentable weight unless the method of obtaining imparts distinct characteristics on the product. See MPEP § 2113(I). Obtaining the introgression segment, which is a DNA segment, by further recombination would not impart specific characteristics on the DNA segment that were not present in the full length WZ introgression segment. Therefore, a plant with a full length WZ introgression segment would also comprise a short WZ introgression segment, just as a plant that was produced by recombination or genome editing to have a short WZ introgression segment and not a full length WZ introgression segment would comprise a short WZ introgression segment.
Shi discloses a N. tabacum plant comprising a Wz introgression segment (abstract). Shi discloses that the full-length WZ introgression segment is approximately 65 Mb long (page 5, right column, paragraph 1). Shi discloses KASP markers for identifying plants comprising the Wz introgression, including KASP-5.1, KASP-10.6, KASP-29.9, and KASP-42.3 specifically (page 4, left column, paragraph 2; table S1). Shi discloses a method of validating Wz-associated SNP markers by extracting DNA from a mapping population of plants comprising the Wz introgression and genotyping plants (page 102, left column, paragraph 4); the plants used for mapping and marker validation were N. tabacum (page 2, right column, paragraph 1).
Woodend provides evidence that the introgression provides resistance to wildfire, caused by Pseudomonas syringae pv. tabaci (page 149, left column, paragraph 2-right column, paragraph 1 & page 150, left column, paragraph 3).
The WZ introgression segment disclosed by Shi comprises within it multiple possible short WZ introgression segments that also inherently comprise sequences positive for the disclosed KASP primer pairs. Thus, a segment of the WZ introgression segment disclosed by Shi that does not comprise a binding site for a KASP-5.1 primer pair and/or a KASP-42.3 primer pair (also disclosed by Shi) because it is shortened by 500Kb anticipates a short WZ introgression segment of the instant invention, and the N. tabacum plant which comprises the full length WZ introgression also comprises a short WZ introgression segment that would test negative for KASP-5.1 and/or KASP-42.3 and positive for KASP-10.6 and KASP-29.9 (claims 1-2). Claim 1 requires that the introgression segment is reduced by a drag gene component and claim 2 requires that the introgression segment has specific test results. The full length WZ introgression segment within the N. tabacum plant disclosed by Shi comprises within it many possible shorter introgression segments which would read on a segment reduced by a drag gene component and return the test results required by claim 2 if the segments were isolated from the N. tabacum plant. Thus, under broadest reasonable interpretation, the N. tabacum plant of Shi anticipates the plants of claims 1 & 2.
Applicant urges that Shi does not disclose a short WZ introgression segment reduced by a drag gene component of at least 500Kb or the defined sequence elements of SEQ ID NOs: 1 and/or 2, and so Applicant urges that Shi’s disclosure does not anticipate the claimed short WZ introgression segment (Remarks, page 17, paragraph 3).
This argument is unpersuasive. Amended claims 1-2 are now drawn to a plant comprising the introgression segment that is reduced in length by defined sequence elements. However, the method by which a segment is “reduced” does not confer functional characteristics; a full length WZ introgression would comprise within its length a segment identical in structure and function to a short WZ introgression that was reduced through recombination. Therefore, the plants of Shi comprising the full length WZ introgression do comprise segment(s) identical in structure and function to a short WZ introgression, including shorter segments that lack SEQ ID NO: 1 or 2. This makes the plants of Shi with the full length WZ introgression not patentably distinct from the plants of amended claims 1-2, so instant claims 1-2 are anticipated.
Applicant urges that claim 2 requires an introgression segment that is positive for KASP-10.6 and KASP-29.9 and negative for KASP-5.1 and/or KASP-42.3, wherein a negative test result indicates that the gene sequences corresponding to the primer pair are to be deleted. Applicant urges that because Shi does not identify any particular short segments or disclose testing to determine that the primer pair should be deleted or retained in tabaci-resistant short WZ introgression segment, the product of claim 2 is not anticipated by Shi (Remarks, page 18, paragraph 2-3).
This argument is unpersuasive, because as presented above, the plants of Shi which comprise a full length WZ introgression segment would also comprise DNA segments that would test positive or negative for the primers as recited by claim 2. Claim 2 does not require that the plant would test negative for a KASP-5.1 primer pair and/or a KASP-42.3 primer pair, just the introgression segment. Since the plants of Shi do comprise portions of the introgression segment that would, taken by themselves in isolation from the rest of the full length introgression segment, inherently test positive or negative for the primers as required by claim 2, the plants of Shi do anticipate the plants of claims 1-2 under broadest reasonable interpretation.
Conclusion
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Victoria L DeLeo whose telephone number is (703)756-5998. The examiner can normally be reached M-Th 7:30am-5pm EST; F 7:30am-12pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Shubo (Joe) Zhou can be reached at (571) 272-0724. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/VICTORIA L DELEO/ Examiner, Art Unit 1662
/Anne Kubelik/ Primary Examiner, Art Unit 1662
Prosecution Insights