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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on Jan. 22, 2026, has been entered. Claim 25 has been canceled. Claims 13-15 and 24 are pending and are examined in this Office Action.
Rejections and/or Objections that are Withdrawn
All rejections of claim 25 are moot in light of Applicant’s cancelation of claim 25.
The objection to claim 13 is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claims 13-15 and 24 under 35 USC 112B for indefiniteness is withdrawn in light of Applicant’s amendments to the claims. It is noted, however, that new indefiniteness rejections are required that were necessitated by Applicant’s amendments to the claims.
The rejection of claim(s) 13-15 and 24 under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Harrweijn is withdrawn in light of Applicant’s amendments to the claims.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.
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”, and 2) “maps to” could be referring to global chromosomal mapping or fine mapping or pin-point mapping, each of which encompass different scopes.
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. If the genomic region extends beyond the two recited sequences on either side, then how far beyond does the region extend?
As to the “maps to” limitation. 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.
Claim 15 recites the limitation "the onion plant" in line 1. There is insufficient antecedent basis for this limitation in the claim because it depends from claim 13 which recites multiple onion plants. Claim 13 recites “at least one onion plant” in line 1, “crossing an onion plant” in line 3, “second onion plant” in line 4, and “a first plant” in line 7; and it is unclear which onion plant claim 15 is referring to.
Claim 24 is indefinite because it recites “a first onion plant”, but it depends from claim 13 which already has a first and a second plant.
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 Jan. 22, 2026, were considered to the extent that they apply to the modified rejection 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, or lack of Complimentary Pinks (CP) bulb color, wherein the QTL maps to:
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; or
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” and the breadth encompassed by “maps to” (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. In the interview summary included by the Applicant, it states the Examiner indicated an amendment to claim 13 “to specify the source materials” would be likely to address the rejection (Resp 4). In the Examiner’s interview 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 either interview summary.
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 13-15 and 24 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a routine use of a product of nature without significantly more. Applicant’s arguments in the response received on Jan. 22, 2026, have been considered to the extent they apply to the amended claims and modified rejection but were not found to be persuasive.
The claims are directed to a method of identifying an onion plant comprising a genotype associated with disease resistance or bulb color by crossing an onion plant with FBR or PR resistance with a second onion plant to produce a population of onion plants, obtaining a sample of nucleic acids from the plant and detecting a polymorphic nucleic acid on chromosome 4. Onion’s chromosome 4 inherently comprises a genomic region with loci comprising different alleles for FBR and PR resistance and for the CP trait. NOTE: the limitations that the resistance “is found” in Serrana or SYG-75-1706 does not mean that either of these two varieties/lines are required to be utilized in any active method steps. It is unclear what it means for the resistance to be “found” in either of these onions (see indefiniteness rejection, above). One interpretation is that the resistance is the same level of resistance. Another interpretation is that the resistance is against the same causative strains/races of pathogen. The alleles can be alleles increasing resistance, decreasing resistance, increasing pink pigment, decreasing pink pigment, or null alleles at the particular locus. Such polymorphic nucleic acids are present, naturally, in the genome of onion plants, and therefor they are considered a judicial exception as laws of nature and natural phenomena (including products of nature) without additional elements that amount to significantly more than the judicial exception (Inventive concept). Detecting such a polymorphism does not amount to significantly more.
MPEP 2106 includes case law about 35 U.S.C. 101 that provides the following:
A correlation between variations in non-coding regions of DNA and allele presence in coding regions of DNA is a natural phenomenon, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1375, 118 USPQ2d 1541, 1545 (Fed. Cir. 2016);
In the limited situation where a process claim reciting a nature-based product is drafted in such a way that there is no difference in substance from a product claim, the claim is subject to the markedly different analysis for the recited nature-based product. These types of claims are drafted in a way that focuses on the product rather than the process steps. For example, consider a claim that recites, in its entirety, "a method of providing an apple." Under the broadest reasonable interpretation, this claim is focused on the apple fruit itself, which is a nature-based product. Similarly, claims to detecting naturally occurring cell-free fetal DNA (cffDNA) in maternal blood were held to be directed to the cffDNA, because the "existence and location of cffDNA is a natural phenomenon [and thus] identifying its presence was merely claiming the natural phenomena itself." Rapid Litig. Mgmt., 827 F.3d at 1048, 119 USPQ2d at 1374, (explaining the holding in Ariosa Diagnostics, Inc. v. Sequenom, 788 F.3d 1371, 115 USPQ2d 1152 (Fed. Cir. 2015)).
Steps of DNA amplification and analysis are not "sufficient" to render claim 1 patent eligible merely because they are physical steps (Genetic Technologies Ltd. v. Merial LLC, 818 F.3d 1369, 1377, 118 USPQ2d 1541, 1547 (Fed. Cir. 2016)).
With regard to dependent claim 14, the step of selecting a plant with the polymorphism is as routine as “providing an apple” or “isolating DNA”.
With regard to claim 15, hybrid, inbred, and progeny plants are all naturally occurring plants and do not amount to “significantly more” than a natural product.
With regard to claim 24, selfing or crossing a selected plant is a routine use.
Therefore, the claimed method requires nothing significantly more than screening a product of nature for a QTL allele and a molecular marker, and routine use of a plant comprising the marker which does not render the claims patent eligible.
Applicant asserts that the claims have been amended consistent with the telephonic interview summary rendering the rejection moot (Resp 6). This is not accurate. In the interview summary included by the Applicant, it states the Examiner indicated an amendment to claim 13 “to include an active breeding step utilizing the QTL source material” would be likely to address the rejection (Resp 4). In the Examiner’s interview summary (mailed Jan. 6, 2026), the Examiner suggested “an active breeding method that utilized Applicant’s deposited onion variety” to overcome the rejection. The amended claims do not require either named onion variety/line to be actively used in the method. The claims do not specify that the deposited onion line is used in an active method step. Therefore, the claims were not actually amended to be consistent with either interview summary.
Summary
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.
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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 1662