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 .
Election / Restrictions
In response to previous the restriction requirement, Applicant has chosen to elect Group I for examination, consisting of claims 1-3, 5 & 16-19, with traverse. Applicant has elected species (i) of the elected group, consisting of SEQ ID NO.1 & 2. New claims 24-26 have been added.
Applicant’s traverse points to a misinterpretation of the Zou reference [Zou, J. et al. Plant Biotechnology Journal (2018) 16, pp.507-519; Published 08-16-2017], cited in response to restriction based on lack of special technical feature. Applicant’s response is directed to the naming of germplasm, arguing that the designation ‘Br-14’ is arbitrary in both disclosures and thus breeding material is not comparable. They point to Zou’s supplemental table 2 indicating the Brassica rapa line ‘Br-14’ is the cultivar ‘Yangyou 2’. This indicates that Zou’s use of Br-14 is not arbitrary, but rather is a code or designation which provides specific information and disclosure to readers about the genetic background which is being referred to and is a source of useful QTL.
Although it is clear what ‘Br-14’ is referring to in the research literature, this does not resolve the issue that Applicant does not provide any information for the germplasm critical to their claimed invention other than its designation ‘Br-14’. One reading Applicant’s patent disclosure, and looking to the relevant literature surrounding B. rapa or interspecific Brassica crosses, would not recognize such a line designation as anything other than the material disclosed by Zou because Applicant has not indicated ‘Br-14’ is an arbitrary designation anywhere in their disclosure, nor indicated in their specification it is not representative of other donor Brassica rapa germplasm designated ‘Br-14’. It is not clearly indicated in the written description that parental material ‘Br-14’ is novel or represents a special technical feature, in the form of unique germplasm not equivalent to that already reported in the peer-reviewed literature and identified by that name. It is also unclear why Applicant would refer to potentially novel and key germplasm in a technical disclosure using a name designation that is the same as, or could reasonably be mistaken for, an existing line code or name designation. Without providing further parentage/pedigree information there is no reasonable indication of what would distinguish Applicant’s ‘Br-14’ germplasm from other breeding material designated similarly.
Applicant additionally argues the novelty of their technical QTL feature, stating that the disclosure does not reference the disease ‘clubroot’ verbatim. However, one skilled in the art would recognize that general studies pointing to sources of potentially valuable genes, such as disease resistance loci identified through common molecular motifs, are not meant to be dispositive or diagnostic for every specific disease they may be used for. Such an assumption would be unrealistic, as disease resistance studies are highly pathogen-specific and require very particular technical execution depending on the disease organism being studied. This does not preclude one skilled in the art from recognizing they could simply further characterize an inherent attribute of a known, previously reported locus, which is routine in the art. However, expanding review of the literature relevant to the instant application uncovers the review of Mehraj [Plants 2020, 9, 726; Published 06-09-2020], which is specific to clubroot and attempts to summarize general knowledge of resistance loci. Therein they point directly to the distal end of chromosome 6A and clearly indicate a clubroot disease resistance QTL which, while minor in comparison to larger effect QTL on A03 and A08, is significant and known as Crr4.
In view of the specification, the claimed invention of the instant application is a disease resistance QTL on chromosome 6A for Brassica, contributed from a Brassica rapa line with no other pedigree or name designation other than ‘Br-14’. Again, the research report of Zou describes use of interspecific Brassica crosses to improve disease resistance, and specifically describes B. rapa introgressions selected on chromosome 6A, contributed by germplasm coded or named as ‘Br-14’. Furthermore, expanded review of the literature presents Mehraj, who clearly points to a clubroot resistance QTL on the distal end of A06, as reported by Suwabe in 2006 [Mehraj, p.4, figure 2]. As such, Applicant has a shared technical feature in their claimed invention in the form of a clubroot or disease resistance QTL on chromosome 6, but it is not a special technical feature due to lack of novelty over previous research reports.
Without further indication of the pedigree or origins of ‘Br-14’ in the instant application on record, the arguments presented surrounding the cited reference are unconvincing. Because of this the inventive categories previously restricted to are maintained for purposes of examination.
Newly added claims 24-26 are drawn to alternate species. Applicant originally disclosed three species, one of which they are required to elect. Applicant has elected species (i) of Group I for examination. The new claims 24-26 are additional non-elected species and therefore are withdrawn from consideration for examination.
Claim Status
Claims 1-3, 5 & 16-19 are under examination on the merits.
Newly added claims 24-26 are withdrawn from consideration.
Priority
Claims 1-3, 5 & 16-19 receive the U.S. effective filing date of 12/21/2020
Information Disclosure Statement
The listing of references in the specification [p.1, 34-35] is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The disclosure is objected to because it contains embedded hyperlinks and/or other form of browser-executable code [p.13 & 24]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claim 1 is objected to because of the following informalities:
Amended claim does not reflect the species election restriction by striking-through or otherwise removing the non-elected species of inventive Group I.
Appropriate correction is required.
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 16-19 are rejected because the claimed invention is directed to a plant or plant part (DNA) containing a naturally occurring allele. Without further indication of the pedigree or origins of ‘Br-14’ in the instant application on record, or indication that the claimed disease resistance allele is anything other than a naturally occurring sequence in existing germplasm, the QTL of the instant application is being interpreted to represent a native, naturally-occurring gene/allele. Sequence comparison of SEQ ID NO. 1 & 2 show them to both have 100% identity to B. rapa genomic DNA sequence disclosed in 2018 [See attached NPL, NCBI Blast Sequence_SEQID1, Sequence_SEQID2, & accession LR031569-1].
The claims recite a plant or part thereof which contains native DNA sequence in the form of a chromosome segment conferring disease resistance or susceptibility. A ‘plant part’ would also encompass the embryo of an identified plant and resulting filial generation, which may or may not contain the allele identified in the parent plant due to genetic segregation. Under such interpretation claims 16-19 would read on any progeny plants, even without the allele of the claimed invention. This judicial exception is not integrated into a practical application because a claim to a naturally occurring allele or DNA sequence conferring disease resistance or susceptibility without further inventive steps does not constitute an invention. Such claims attempt to claim a naturally occurring gene through its technical description. They also claim descendant Brassica plants with potentially any genetic background, absent the described disease resistance allele. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they simply claim a naturally occurring genetic allele, described as a QTL, without further inventive steps beyond the gene’s inherent properties of disease resistance.
Because of this, claims 16-19 are rejected in their entirety.
Claims 1-3, 5 & 16-19 are rejected because the claimed invention is directed to detection or diagnosis of a naturally occurring phenomenon without significantly more. Without further indication of the pedigree or origins of ‘Br-14’ in the instant application on record, or indication that the claimed disease resistance allele is anything other than a naturally occurring sequence in existing germplasm, the QTL of the instant application is being interpreted to represent a native, naturally-occurring gene/allele. Sequence comparison of SEQ ID NO. 1 & 2 show them to both have 100% identity to B. rapa genomic DNA sequence disclosed in 2018 [See attached NPL, NCBI Blast Sequence_SEQID1, Sequence_SEQID2, & accession LR031569-1].
The claims 1-3 & 5 recite a method of identifying a plant or part thereof which contains native DNA sequence in the form of a genetic locus conferring disease resistance or susceptibility. This judicial exception is not integrated into a practical application because diagnosis of a gene or allele conferring disease resistance or susceptibility without further inventive steps does not constitute an invention. Further claims are drawn to ‘detection of the QTL’ (claim 1) or ‘genotyping’ (claim 3 line 3), which in the case of this particular gene, could be accomplished simply by phenotypic observation of diseased or healthy plants. Such claims would encompass observation and recording of clubroot response of potentially any Brassica exposed to clubroot through routine field observation and scoring of disease incidence. These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they simply point to diagnosis/identification of plants carrying a native DNA sequence and the inherent properties of that individual, as would be expected from genetic testing. Dependent claims 16-19 are drawn to individual plants diagnosed with such methods.
Because of this, claims 1-3, 5 & 16-19 are rejected.
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.
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 1-3, 5 & 16-19 are rejected under 35 U.S.C. 103 as being unpatentable over Mehraj [Plants 2020, 9, 726; Published 06-09-2020] in view of Suwabe [Genetics 173: 309–319 (May 2006); Published 05-01-2006] and Zhang [Mol Breeding (2014) 34:1173–1183; Published 05-17-2014].
Mehraj reviews known sources of clubroot resistance and use in their 2020 review, “Genetics of Clubroot and Fusarium Wilt Disease Resistance in Brassica Vegetables: The Application of Marker Assisted Breeding for Disease Resistance”. Specifically, they disclose sources of Plasmodiophora resistance in B. rapa including those on the distal end of chromosome A06 [p.4, Figure 2]. They indicate previous discovery of a “major CR [clubroot resistance] loci” known as Crr4 and linked to marker WE24-1 described by Suwabe. Mehraj goes on to teach the use of that information, development of markers for identifying and selecting improved disease-resistant Brassica [p.9, par.1, ‘Resistant Breeding, Gene Accumulation, and MAS].
Mehraj’s review does not specify sequences linked to clubroot resistant QTL on chromosome A06, or the specifics of fine-mapping and providing improved markers for previously disclosed clubroot resistance QTL.
However, this is remedied by Suwabe and also through the teachings of Zhang. Suwabe provides the original disclosure of clubroot-resistant loci specific to the distal end of chromosome A06, initially described as Crr4 in 2006, “this small QTL was independent of Crr1, Crr2, and Crr3…it is in fact a novel resistance locus and is designated Crr4” [p.311-313, ‘QTL Analysis for clubroot resistance’]. Their supplemental data table provides a sequence for the linked marker WE24-1, and graphically depicts the location of this QTL marker at 7.1 cM from the distal end of chromosome A06 [p.312, Figure 1, linkage group ‘2 (R6)’]. Applicant’s disclosure depicts the site of their clubroot resistance QTL as occurring between 5 – 7.5 Mbp from the distal end of chromosome A06 [p.312, figure 1]. While conversion between linkage distances reported as centimorgans into physical distances reported as base pairs is inexact, estimates of distance relationships in Brassica have been reported as 1cM generally being equivalent to 500kb [Suwabe, p.311, col.1, par.4]. Conversion to estimated linkage distances place WE24-1 at 7.1cM and Applicant’s claimed SEQ ID NO.1 marker bounds at 7.4cM, with estimated difference of 0.3cM, indicating a high probability of linkage or similar causative gene(s) defining the two loci. The small variability in estimated genetic distance may be due to a variety of factors, including the different breeding populations tested [See Brown, TA; Genomes 2nd ed, Chapter 5.2.3, ‘From partial to linkage to genetic mapping’, Figure 5.22; and Vinod, Kosambi and the genetic mapping function. Reson 16, 540–550 (2011)]. It is within reason to interpret the co-localization of QTL associated markers as indicating the claimed markers, specifically the boundary marker of SEQ ID NO.1, of the instant application are closely linked to, and reasonably within the bounds of the previous Crr4 clubroot resistance locus on A06.
Suwabe does not provide additional markers near WE24-1 associated with the Crr4 QTL region, likely due to technical limitations of genotyping or bioinformatics resources in 2006. Despite this lack of resolution based on technical limitations at the time of initial disclosure by Suwabe, they clearly point to this region and the later and now-routine procedure of fine-mapping QTL is clearly taught by Zhang. In Zhang’s 2014 research report on characterizing the CRb QTL of chromosome A03, they walk through the specific procedures used to go from an initial disclosure of a target clubroot-resistance QTL region, such as in Suwabe, to a fine-mapped description of sequences to be used as additional markers. This teaches the methods of arriving at the genetic markers claimed of the instant application, drawn to sequences that appear to be linked to the previously disclosed Crr4 QTL in Suwabe.
Researchers with ‘an ordinary level of skill’ working in this field typically have specialized training directed to performing searches of the scientific literature and cross-applying methods and genetic information from different areas of related research. Because of the high level of training and creativity presented by those of ‘ordinary’ skill in the art, one would plainly see the advantages of fine-mapping previously disclosed clubroot resistance QTL, as outlined by Zhang, when combined with prior knowledge of the general location of such QTL on chromosome A06 of B. rapa taught by Suwabe. One would be motivated to combine these disclosures in order to provide a more granular description of various alleles and molecular markers associated with Crr4 that may be valuable to breeding. They would want to do this because identifying and applying such disease resistance genes would have obvious agronomic and economic value, as clearly summarized and presented by Mehraj. It was known in the art that a minor clubroot resistance allele is present on the distal end of A06 as QTL Crr4, that fine-mapping was routinely used to provide improved technical description of such known QTL, and that a refined description of Crr4 or other minor QTL known on chromosome A06 would be a way to effectively repeat successes previously demonstrated for the more prominent clubroot resistance QTL on A08 & A03, such as clearly taught for CRb by Zhang.
Because providing such refined sequence description(s) of the previously known, native A06 clubroot resistance QTL associated with Crr4 would be obvious in view of prior art, claims 1-3, 5 & 16-19 are rejected in their entirety.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad 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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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/ SPE, Art Unit 1663 Request for Information under 37 CFR § 1.105
Applicant and the assignee of this application are required under 37 CFR § 1.105 to provide the following information that the examiner has determined is reasonably necessary to the examination of this application.
This request is being made for the following reasons:
Applicant’s invention is drawn to claims requiring use of a Brassica rapa donor line ‘BR-14’, but the instant specification is silent about the source of donor line ‘BR-14’. The requested information is required to make a meaningful and complete search of the prior art.
In response to this requirement, please provide answers to each of the following interrogatories eliciting factual information:
(i) What is the germplasm source and pedigree of ‘BR-14’? Please supply all of the designations/denominations used for this line.
(ii) At or before the time of filing of the instant application or any provisional application to which benefit is claimed, had said ‘BR-14’ been disclosed or made publicly available? If so, under what designation/denomination and under what conditions were said strain been disclosed or made publicly available and from when to when?
If Applicant views any or all of the above requested information as a Trade Secret, then Applicant should follow the guidance of MPEP § 724.02 when submitting the requested information. If any part of the response is marked DO NOT SCAN or TRADE SECRET, Applicant is reminded that a cover letter, not so marked, is to be included.
In responding to those requirements that require copies of documents, where the document is a bound text or a single article over 50 pages, the requirement may be met by providing copies of those pages that provide the particular subject matter indicated in the requirement, or where such subject matter is not indicated, the subject matter found in applicant' s disclosure. Please indicate where the relevant information can be found.
The fee and certification requirements of 37 CFR § 1.97 are waived for those documents submitted in reply to this requirement. This waiver extends only to those documents within the scope of this requirement under 37 CFR § 1.105 that are included in the applicant' s first complete communication responding to this requirement. Any supplemental replies subsequent to the first communication responding to this requirement and any information disclosures beyond the scope of this requirement under 37 CFR § 1.105 are subject to the fee and certification requirements of 37 CFR § 1.97.
The applicant is reminded that the reply to this requirement must be made with candor and good faith under 37 CFR § 1.56. Where the applicant does not have or cannot readily obtain an item of required information, a statement that the item is unknown or cannot be readily obtained may be accepted as a complete reply to the requirement for that item.
This requirement is an attachment of the enclosed Office action. A complete reply to the enclosed Office action must include a complete reply to this requirement. The time period for reply to this requirement coincides with the time period for reply to the enclosed Office action.
/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663