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 .
Claims
Applicant's submission filed on May 26, 2026, has been entered. Claims 13-15 and 24 are pending and are examined in this Office Action.
Rejections and/or Objections that are Withdrawn
The portion of the indefiniteness rejection under 35 USC 112(b) that is directed to claim 15 reciting a limitation that lacks antecedent basis is withdrawn in light of Applicant’s amendments to the claims.
The portion of the indefiniteness rejection under 35 USC 112(b) that is directed to claim 24, specifically, is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claims 13-15 and 24 under 35 U.S.C. 101 is withdrawn in light of Applicant’s amendments to the claims.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.
Claims 13-15 and 24 are 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. All dependent claims are included in this rejection unless they include a limitation that overcomes the deficiencies of the parent claim. Applicant’s arguments in the response received on May 26, 2026, has been fully considered but is not found to be persuasive.
Claim 13 recites “wherein said resistance to FBR is found in onion variety Serrana” and “resistance to PR is found in onion line “SYG-75-1706”. It is unclear what this means. Does this mean the onion plant used in the cross must have the same level of resistance as Serrana/SYG-75-1706? Does this mean it needs to be resistant to the same strains of Fusarium that cause FBR when compared to Serrana/SYG-75-1706? Does this mean it needs to have the same resistance gene(s) as Serrana/SYG-75-1706? Does this mean it needs to have the same allele(s) of the same gene(s) as Serrana/SYG-75-1706? It is unclear what a given onion would need to have to satisfy this requirement for the claims.
Claim 13 requires the limitation that the QTL “maps to” an onion genomic region “defined by and comprising” recited sequences. This claim is indefinite because it is unclear how close the QTL would need to be to the recited sequences on the chromosome for two reasons: 1) the genomic region is “defined by and comprising” the recited sequences, but it is unclear how much genomic region outside of the pair of sequences is encompassed by “defined by and comprising”.
As to the genomic region, one interpretation could be that the region begins precisely at the first recited sequence and ends precisely at the second recited sequence and includes all nucleotides in between the two recited sequences. But, the interpretation could also be interpreted to include the two recited sequences and everything in between but to also extend beyond these sequences on either side. The word “comprising” is open language that is inclusive of more than just the recited sequences, and the claim does not clearly limit the additional genomic DNA to be only genomic DNA that is in between the two recited marker sequences. If the genomic region extends beyond the two recited sequences on either side, then how far beyond does the region extend?
If Applicant intends the claim to require that the QTL and the polymorphic nucleic acid lie on the chromosome in between the two recited sequences, then the claim should be amended to clearly require this. If the Applicant intends the claim to encompass something beyond having the QTL and the polymorphic nucleic acid lie on the chromosome in between the two recited sequences, then the claim should be amended to clarify the intended scope. Currently it is completely unclear how large the “genomic region” is and it is completely unclear how close the QTL would need to be for it to map to this region.
Applicant argues that the phrase “is found in” only requires that the onion plants used in the cross of step (i) possess FBR or PR resistance that is characteristic of the resistance identified in Serrana and SYG-75-1706, respectively, as characterized in the specification. Applicant gives examples of what “characteristic of” can be as “derived from” or “equivalent to”. This reenforces the Examiner’s position that it is unclear what would be required to be “characteristic of” because what aspects of the resistance would be required to be considered “equivalent to” the resistance in Serrana or SYG-75-1706? And when something is “derived from” a starting material, it means part of the starting material is retained and/or modified and part is discarded. It is unclear what part of Serrana or SYG-75-1706 would be required to be retained. (resp 5)
Applicant argues that claim 13 has been amended to change “maps to “ with “is located within” (Resp 5-6). This does not remove the indefiniteness, because it remains unclear if the region that is “defined by and comprising” the two markers is limited to the genomic region with the two marker sequences as the end points, or if the genomic region can extend beyond either of these markers on either side.
Inadequate 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 13-15 and 24 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. All dependent claims are included in this rejection unless they include a limitation that overcomes the deficiencies of the parent claim. This rejection has been modified to address the amendments to the claims. Applicant’s arguments in the response received on May 26, 2026, were considered but were not found to be persuasive.
The claims are broadly drawn to a method of identifying (claim 13) and selecting (claim 14) at least one onion plant comprising a genotype associated with disease resistance or bulb color, the method comprising the steps of: (i) crossing an onion plant comprising resistance to Fusarium basal rot (FBR) or Pink Root (PR) with a second onion plant to produce a population of onion plants, wherein said resistance to FBR is found in onion variety Serrana and said resistance to PR is found in onion line SYG-75-1706, a sample of seed of said line having been deposited under NCMA Accession No. 202112015; (ii) obtaining a sample of nucleic acids from a first plant or part thereof from said population; and (iii) detecting in said sample the presence of an allele of at least one polymorphic nucleic acid that is in or a Quantitative Trait Locus (QTL) associated with FBR resistance, PR resistance, and lack of Complimentary Pinks (CP) bulb color, wherein the QTL is located within:
an onion genomic region defined by and comprising SEQ ID NO:3 and SEQ ID NO:23 on linkage group 2 (LG2), conferring resistance to FBR;
an onion genomic region defined by and comprising SEQ ID NO:22 and SEQ ID NO:27 on LG2, conferring resistance to PR; and
an onion genomic region defined by and comprising SEQ ID NO:26 and SEQ ID NO:29 on LG2 conferring lack of the CP bulb color; including wherein the onion plant is an agronomically elite plant, a hybrid, or an inbred (claim 15), and including wherein the method further comprises selecting a plant comprising said allele and self-pollinating the plant (claim 24).
Applicant describes onion plants that are F3 progeny from a cross between onion variety “Serrana” and onion variety “SYG-75-1706” wherein the F3 progeny comprise a fragment of LG2 (chromosome 4) from Serrana that confers partial resistance to FBR and comprises SEQ ID NO: 7 with an “A” at the variable position and SEQ ID NO: 17 with a “G” are the variable position, and a fragment of chromosome 4 from SYG-75-1706 that confers partial resistance to PR and comprises SEQ ID NO: 23 with a “C” at the variable position and SEQ ID NO: 27 with a “G” at the variable position (see table on page 26 of the specification and see fine mapping data in Example 5 and Table 4 and Table 2). They describe a genomic region on chromosome 4 of SYG-75-1706 that comprises the Complementary Pinks (CP) trait and comprises SEQ ID NOs: 27 and 28 with a “G” at each of the variable positions (See Table 4).
Applicant describes SEQ ID NOs: 1-29 as marker sequences for Marker assisted selection (MAS) and fertile x fertile cross (FxF) workflow for distinguishing between SYG-75-1706 genomic DNA and Serrana genomic DNA on LG2 (chromosome 4) (Spec 31-6). Applicant describes SEQ ID NOs:75-98, 116-139, 157-180, and 198-221 as probe and primer sequences for Taqman(R) assays for identifying polymorphic markers capable of distinguishing between SYG-75-1706 genomic DNA and Serrana genomic DNA on LG2 (chromosome 4) (Spec 44-7). Methods for performing Taqman(R) assays are well known in the art and are routine. Methods for detecting single nucleotide polymorphisms, such as the ones described in SEQ ID NOs: 1-29 are well known in the art and are routine.
Applicant describes markers in Table 4 for detection of genomic regions from linkage group 2 (chromosome 4) of SYG-75-1706 onions and Serrana onions that are associated with resistance to FBR and PR and presence/absence of the CP trait. This region of linkage group 2 (chromosome 4) is described as spanning 21.8 cM in genetic mapping distance, with the FBR locus in a region of 12.2 cM, the PR locus in a region of about 0.5 cM, and the CP locus in a region of at least 0.6 cM with the PR locus positioned in between the FBR and CP loci (Spec 52, Table 4). Applicant describes selecting onions based on desired genotype data associated with FBR resistance in Serrana onions (Spec 24, 51).
Applicant does not describe any onion plant comprising resistance to FBR that is “found in variety Serrana” other than Serrana onions themselves. Applicant does not describe any onion plant comprising resistance to PR that is “found in onion line SYG-75-1706” other than SYG-75-1706 onions themselves.
Applicant does not describe any polymorphic nucleic acids other than SEQ ID NOs: 1-29 which comprise SNPs that distinguish between Serrana and SYG-75-1706 genomic DNA. The claims encompass detection of any polymorphic nucleic acid on a region of undefined size on chromosome 4 because of the indefiniteness around the breadth of the “genomic region” (see indefiniteness rejection, above). Table 4 shows that the region of chromosome 4 comprising the FBR and PR resistance alleles and the allele conferring the CP trait spans about 21.9 cM, and it is unclear if this entire region would be considered a region “defined by and comprising” each of the recited pairs of sequences, or if the required genomic region would be even larger than this, or if the required genomic region would be limited to some fragment within this region. Given that Serrana and SYG-75-1706 varieties are not closely related genetically, there will be multitudes of polymorphisms between these two varieties across the breadth of genomic DNA contained in this large of a segment of chromosome 4. 29 described SNPs is not sufficient to be representative of the extremely large genus of markers encompassed by the claims.
Applicant does not provide polymorphic nucleic acids from this region of chromosome 4 that distinguish between any onion varieties other than Serrana and SYG-75-1706. It is known in the art that “there is no guarantee that DNA markers identified in one population will be useful in different populations, especially when the populations originate from distantly related germplasm” (Collard et al. (2005) Euphytica; Vol. 142; pp. 169-196; especially page 186). For markers to be useful, more generally, in breeding programs, then they would need to be validated and shown to reveal polymorphisms in different populations derived from a wide range of different parental genotypes (Collard et al., page 186). Applicant has not described any validation of their particular polymorphic nucleic acids with any other onion germplasm. A description of 29 SNPs that can distinguish Serrana genomic DNA from SYG-75-1706 genomic DNA is not sufficient to be representative of SNPs effective for distinguishing genomic DNA between the vast number of varieties/cultivars encompassing all other onion germplasm.
For the reasons set forth, above, the instant application has not provided an adequate description of the broadly and generically claimed materials to be used in their method.
Applicant traverses the rejection, but does not present any grounds for the traversal (Resp 6), therefore, the Examiner is unable to respond.
Applicant asserts that the claims have been amended consistent with the telephonic interview summary rendering the rejection moot (Resp 6).
This is not accurate with regard to the written description rejection. In the interview summary included by the Applicant, it states the Examiner indicated an amendment to claim 13 require detection of a plant with both FBR and PR resistance would overcome the rejection under 35 USC 101 and possibly the written description (Resp 4).
The Examiner agrees that the amendments overcome the rejection under 35 USC 101, but the amendments do not overcome the written description rejection.
In the Examiner’s interview summary for the previous interview which took place on Jan. 2, 2026, (summary mailed Jan. 6, 2026), the Examiner suggested “a breeding method that begins with crossing the SYG-75-1706 onion of the Serrana onion with a different onion and using the markers to detect the introgression” of the resistance allele from that particular germplasm.
The amended claims do not require either named onion variety/line to be actively used in the method. The claims do not specify the source materials other than requiring the source materials to have resistance to the disease(s). Therefore, the claims were not actually amended to be consistent with the previous interview summary, and the most interview summary did not include any discussion of the written description rejection, but merely said the suggested amendment would be a step in the right direction.
Summary
THIS ACTION IS MADE FINAL. 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.
No claim is allowed.
Examiner’s Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHY KINGDON whose telephone number is (571)272-8784. The examiner can normally be reached M-F 9:00 - 5:30 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, Amjad A Abraham can be reached on (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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CATHY KINGDON
Primary Examiner
Art Unit 1663
/CATHY KINGDON/Primary Examiner, Art Unit 1663
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