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
Applicant claims priority to provisional application 63/378320 filed on 10/04/2022
Status of the Claims
Claims 1-2, 5-9, 11-15, and 18-25 are pending.
Claims 1-2, 5-9, 11-15, and 18-25 are examined herein.
Specification
The specification is objected to for reciting terms that are undefined. For example:
Paragraph 122 recites “ADF” which is not defined;
Paragraph 123 recites a “DH population” which is also not defined.
The applicant is encouraged to review the specification for more undefined terms.
Information Disclosure Statement
The specification contains references throughout the document (see paragraphs 5, 6, and 64 for examples) that are not listed on a proper IDS. Unless the references are in the IDS document filed on 06/26/2025 or on the PTO-892 form, the references have not been considered.
Claim Interpretation
Claim 14 line 6 recites “SEQ ID NO:79 (N101HGY-001)” which appears to be a typo as SEQ ID NO:78 is N101HGY-001 as was recited in Claims 1 and 11 and Table 7.
Chromosome N15 appears to be an arbitrary name assigned by the applicant and may be identified by a different name in other literature or prior art.
Fiber in Brassica Napus consists of NDF (neutral detergent fibre), ADF (acid detergent fibre) and ADL (acid detergent lignin) according to page 1 paragraph 1 Behnke, Nina, Edy Suprianto, and Christian Möllers. "A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.)." Theoretical and Applied Genetics 131.11 (2018): 2477-2492.
The deletion start/end break points referenced in Claim 8 and “break points” in Claim 22 is interpreted to be the nucleotides on either side of the WT DNA (without insertion or N15 deletion) of chromosome N15 that comes into contact with the inserted nucleotides. Additionally, SEQ ID NOs: 80-83 are interpreted by the examiner to be nucleotide sequences that map/span these regions where DNA was deleted and inserted and does not map to WT that does not have the N15 deletion and insertion.
Genomic Positions 86.09 cM and 101.53 cM are interpreted by the examiner to be the same regions as SEQ ID NOs:65 and 78 (see table 5) of the specification.
Claim Objections
Claim 1 is objected to for omitting “a” between “for” and “genomic” in line 5.
Claim 2 is objected to for omitting “the” between “in” and “genomic” in line 2.
Claim 6 is objected to for omitting a space between SEQ ID NO:83 and respectively.
Claim 7 is objected to for reciting “any one of” in line 1 which should be removed.
Claim 7 is objected to for omitting “an” between “of” and “insertion”.
Claim 8 is objected to for reciting “for insertion of replacement” which should be replaced with “for an insertion of a replacement”.
Claim 11 is objected to for omitting “a” between “for” and “genomic” in line 8.
Claim 15 is objected to as it requires “of” between “method” and “screening” in line 1 and should include “the” between “in” and “genomic” in line 2.
Claim 19 is objected to for reciting “any one of” in line 1 which should be removed.
Claim 20 is objected to for reciting “any one of” in line 1 which should be removed and should include “an” before “insertion” in line 2.
Claims 21-22 are objected to for reciting “any one of” in line 1 which should be removed.
Claim 23 is objected to for omitting “the” between “with” and “method” in line 9.
Claims 23-24 are objected to for reciting “Brassica” which should be “Brassica”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 1-2, 5-9, 11-15, and 18-25 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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.
Claims 1-2, 5-9, 11-15, and 18-25 are rejected for indefiniteness because of the ambiguity as to the exact location the deletion and optional insertion are located. While the claims give limitations as to characteristics of the location of the arbitrarily named chromosome “N15”, the described limitations do not necessarily limit the encompassed subject material to one location within the chromosome.
Claims 7-8 and 20 are rejected for reciting methods that detects an insertion events that occurred in the N15 deletion. This makes it unclear if the WT plant detected in independent Claims 1 and 14 (which has the original sequence in the deletion site) can be selected for in step c.
Claim 8 is rejected for lack of antecedent basis as it references a “replacement sequence” which is not referenced in any of the prior claims. What is a replacement sequence? Is it the same as the deleted WT sequence?
Claims 5 and 18 are rejected for reciting “about” which does not clearly define the length of the deleted sequence. One with ordinary skill in the art studying this vast region of the chromosome would not have any indication if another segment of deleted DNA is “about” 1,667 kb. Is 3,000 kb or 1000 bp about 1,667 kb?
Claims 6,8 and 19, are rejected for reciting “respectively”. It is unclear if this word refers to the sequences or locations.
Claim 14 line 6 recites “SEQ ID NO:79 (N101HGY-001)”. SEQ ID NO:79 is identified as N101HJK-001 while N101HGY-001 is identified as SEQ ID NO:78 in table 7. Thus, the claim is indefinite, and it is unclear if it is referencing SEQ ID NO 78 or 79.
Claim 14 is also rejected for lack of antecedent basis as it references “the one or more low fiber content marker alleles”. The independent claim has only referenced a deletion associated with low fiber content.
Claim 22 is rejected for being indefinite because it is unclear to the examiner what is being amplified or sequenced. It recites the sequencing/amplification can start from 10 to 300 bases from a break point but does not indicate what direction or how long the DNA being sequenced/amplified has to be. Is it amplifying the deleted region?
Claim 25 is indefinite because a breeding strategy for reduced fiber content would produce plants with reduced fiber content (i.e. an agronomic characteristic) when compared to the recurrent patent, if the selected recurrent parent did not contain the N15 deletion and had higher fiber content.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 23-25 are rejected under 35 U.S.C. § 112(d), as being of improper dependent form for failing to further limit the subject matter of the claim upon which they depend, or for failing to include all the limitations of the claim upon which they depend.
The independent and referenced Claim 1 is drawn to a method for selecting a Brassica napus plant.
Claims 23-25 are directed to a method of introducing a low fiber content trait into any Brassica plant by crossing a parent Brassica plant comprising the N15 deletion with a second parent plant that does not comprise the N15 deletion, then performing backcrossing. Thus, Claims 23-25 fail to further limit the subject matter of Claim 1. Claims 23-25 fail the infringement test because Claims 23-25 would conceivably be infringed by performing such a method in another Brassica species other than Brassica napus, which would not infringe Claim 1. See MPEP § 608.01(n).
Applicants may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent
form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent
claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
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 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.
Claims 1-2, 5-9, 11-15, 18-25 are rejected under 35 U.S.C. 103 based on the teachings of WO 2020/131600 A1 (Agrigenetics) (See IDS filed on 09/25/2026) in view of NC_063448.1 and Wang, Jia, et al. "Genome-wide analysis of seed acid detergent lignin (ADL) and hull content in rapeseed (Brassica napus L.)." PLoS One 10.12 (2015): e0145045 (See IDS filed on 09/25/2026).
Claims 1-2, 5-9, 11-15, and 18-25 are drawn to methods of selecting/producing a Brassica napus plant, germplasm or grain thereof that comprises a low fiber content trait. The phenotype is associated with a deletion in the N15 chromosome that can also contain an insertion event. The methods are also directed to crossing selected plants and performing backcrosses to breed for a plant with decreased fiber content.
Agrigenetics is directed to “methods and compositions for identifying canola plants that have a low fiber content trait…. Some embodiments concern molecular markers to identify, select, and/or construct low fiber content canola plants and germplasm, or to identify and counter-select plants with relatively higher fiber content”. Markers are defined in paragraph 55 which recites markers can be deletions or insertions and are polymorphisms that vary between individuals of the same species. Thus, the N15 deletion and optional insertion to be a marker. Immediate and independent Claims 1, 11, and 14 are drawn to methods of selecting/producing a Brassica napus plant, germplasm or grain thereof that comprises a low fiber content trait which comprises: a) obtaining/isolating a nucleic acid samples from one or more Brassica napus plant, germplasm, or grain, b) screening each sample for genomic sequences comprising a deletion on a chromosome called N15 and c) selecting one or more plant, germplasm, or grain, from the population comprising the deletion. The samples can represent a plurality of other plants, germplasms, or grains (i.e. Claim 11) and/or be used in a cross to generate progeny plants that also comprise the low fiber content marker (i.e. deletion) as recited in Claim 14. These limitations (i.e. method steps of extracting nucleic acids, selecting plants with a desirable marker/QTL) are taught in paragraphs 9, 13, 17 and 22 and Claims 1, 8, and 13 of Agrigenetics. Agrigenetics also teaches “Markers (i.e. deletions/insertion) corresponding to genetic polymorphisms between members of a population can be detected by methods known in the art. These include, but are not limited to, nucleic acid sequencing (immediate Claims 9 and 21-22). Regarding Claims 12 and 13, paragraph 44 teaches "germplasm" (tissue where nucleic acid sample is extracted) refers to cells of a specific plant; seed (i.e. grain; i.e., instant Claim 12). Additionally, Agrigenetics teaches meal made from such methods in paragraph 12 and claims 12 and 19. Paragraph 42 of Agrigenetics teaches backcrossing techniques (i.e. crossing parent Brassica plant with low fiber content marker with a brassica plant without it and the crossing the desired progeny to the recurrent parent multiple times) which were limitations of instant Claims 23-25. Additionally, paragraph 101-102 teaches the methods outlined in the disclosure can be used to transfer nucleic acid sequence (i.e. low fiber content trait) from a low fiber content donor canola plant into a high fiber content recipient canola plant by crossing the plant and using traditional breeding techniques along with marker-assisted selection and marker-assisted breeding (requiring obtaining a nucleic acid sample from progeny) and further teaches the limitations of instant Claims 23-25.
While Agrigenetics teaches methods of selecting/producing a Brassica napus plant, germplasm or grain thereof that comprises a low fiber content traits (i.e. deletion/insertion markers) and using such methods like backcrossing, it does not recite the use of such methods for the N15 chromosome and N15 deletion between genomic positions corresponding to SEQ ID NO:65 (N101 HTV-001) and SEQ ID NO: 78 (N 101 HGY-001) and wherein the N15 deletion is associated with low fiber.
NC_063448.1 is chromosome C5 from Brassica napus from NCBI assembled in 2019 and appears to be last updated on 23-June-2022. NC_063448.1 teaches the sequences SEQ ID NOS: 65, 78, and 82-83 (i.e. Claims 1, 6, 8,11,14 and 19) (see below). The sequences appear to map to a region between 51,056018-5296329 on NC_063448.1. This is a location and segment similarities to Applicant’s chromosome N15 (see Specification paragraphs 10,134, and table 6). Thus, Applicant’s N15 chromosome appears to be identical to C5 in NC_063448.1 and the N15 deletion would be between positions 51,056018 and 5296329. Because the NC_063448.1 sequence contains SEQ ID NOs:82-83, the examiner interprets this chromosome to be comparable to the NS8290BC elite line referenced in the specification in paragraph 134 and table 6 which contains a 1.1 Mb insertion segment, and contains a ~1,667 kb insertion as that is the distance between SEQ ID NOs:82-83 (i.e. Claims 5 and 18).
While Agrigenetics teaches the methods of selecting/producing a brassica napus plant, germplasm or grain thereof that comprises a low fiber content traits and NC_063448.1 teaches the sequences, they do not teach this particular region’s association with fiber content.
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SEQ ID NO: 65
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SEQ ID NO: 78
SEQ ID NO: 82
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SEQ ID NO: 83
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Wang et al 2015 is directed to genome-wide association analysis (as was performed in example 2 of the specification) of 520 accessions of Brassica Napus with 31,839 single-nucleotide polymorphism (SNP) (see abstract). Page 2 paragraph 3 teaches “correlation between seed color and fiber composition has been observed, particularly with the amount of acid detergent lignin (ADL)”. The Abstract and page 5 paragraph 3 also teaches the B. napus chromosome C05 is associated with ADL (i.e. fiber). Table 3 teaches chromosome C05 has multiple candidate genes (BnaC05g42520D, BnaC05g42570D, BnaC05g42630D, BnaC05g43530D and BnaC.MYB83) identified by markers/SNP(s) rs37369 and rs37408 associated with seed ADL (i.e. fiber) content. These two markers (sequences from supplementary table 4) appear to map between positions 51,056018 and 5296329 of NC_063448.1 i.e. (SEQ ID NOs:65 and 78). Therefore, the method performed by Wang et al 2015 that uses markers/SNP(s) rs37369 and rs37408 that map between SEQ ID NOs:65 and 78 were used to detect deletions which meets the limitations of Claims 1, 11, and 14. The method performed by Wang et al 2015 that used markers/SNP(s) rs37369 and rs37408 that map between SEQ ID NOs:82 and 83 (i.e. contains an insertion into the N15 chromosome deletion) and were used to detect insertion sequences which meets the limitations of Claims 7-8, and 20. Regarding claims directed to screening for the absence of markers between 86.09 cM and 101.53 cM or between SEQ ID NOs: 82-83, the method of Wang et al 2015 which uses SNPs/markers (i.e. rs37369 and rs37408) would not map to WT C15 (without insertion) as would not have the sequences associated with the break points (SEQ ID NOs:81-82). Thus, screening for the absence of these markers mapping between 86.09 cM and 101.53 cM or between SEQ ID NOs: 82-83 would indicate the deletion event did not occur (i.e. Claims 2,6,15, and 19).
SNP TS37408
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SNP TS 37369
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It would have been prima facie obvious to combine the teachings of Agrigenetics in view of NC_063448.1 and Wang et al 2015 to develop methods for selecting/producing a Brassica napus plant, germplasm or grain thereof that comprises a low fiber content trait. All references are directed to Brassica napus plants while Agrigenetics and Wang et al 2015 are directed to breeding for reduced fiber content in Brassica napus. Wang et al 2015 and others1 teach this region is a known QTL associated with fiber content, and it would have been obvious to one of ordinary skill in the art to use markers/SNPs/fine mapping to identify/track this QTL and identify sequences from NCBI or sequencing results. Methods for crossing/backcrossing plants for lower fiber are also well known in the art and described in Agrigenetics, which also provides the motivation in paragraphs 2 and 4, which teaches that lower fiber is a desirable nutritional trait in Brassica napus. The decision to look for the absence/presence of the markers between any specified sequences within this particular region known to be associated with low fiber content (i.e. Claims 2,6,15, and 19), generating meal from the selected plurality of grains (i.e. Claim 12) or preparing canola meal from one or more of the selected plants/germplasm/grain (i.e. Claim 13), or where to amplify/sequence (i.e. Claim 32) are mere design choices as the criticality has not been demonstrated by the Applicant and would have been obvious to one of ordinary skill in the art. Additionally, the deletion segment size (is inherent to the invention) and not an inventive step (i.e. Claims 5 and 18).
Even if it is determined that Agrigenetics in view of NC_063448.1 and Wang et al 2015 do not explicitly teach each limitation in the instant claims, the use of SNPs/markers to identify/track QTLs (including fiber content QTLs) and use them for selecting germplasms are well known in the art and common practices, absent evidence to the contrary. Additionally, this region of the chromosome is known to be rich in QTLs associated with fiber content2 and “ segmental exchanges [deletions/insertions] between homeologous chromosomes are frequent throughout the B. napus genome” (see page 1 paragraph 1 of Stein, Anna, et al. "Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus." Plant biotechnology journal 15.11 (2017): 1478-1489).
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GEORGE W MEYER whose telephone number is (571)272-3733. The examiner can normally be reached Monday - Friday 8:00 am- 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/GEORGE W MEYER/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Behnke, Nina, Edy Suprianto, and Christian Möllers. "A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.)." Theoretical and Applied Genetics 131.11 (2018): 2477-2492.
2 Behnke et al 2018 and Wang et al 2015.
