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 27-29 have been added.
Applicant’s traverse points to the difference between their ‘Br-14’ designated line and others reported as ‘Br-14’ [Remarks, p.8, ¶.7]. In view of Applicant’s response to the 105 request/interrogatories mailed 30 July 2025, it is now clear their material is representative of the known clubroot resistant germplasm ECD-04 [Applicant response, p.2, ¶.2-3].
Applicant’s argument is unconvincing because the disclosure of the source of the internally coded ‘Br-14’ now indicates the source of the allele is ECD-04. The germplasm ECD-04 is a widely known and used source of naturally occurring alleles for clubroot resistance [See Abstract in Yang Plant Biotechnology Journal (2022)20, pp. 1502–1517; Published 10 Apr 2022, and, Dixon (2026) The Journal of Horticultural Science and Biotechnology, 101:4, 481-495; Published 31 Mar 2026]. As such, the technical feature of a locus conferring clubroot resistance, from a plant of the ECD-04 population, is not a special technical feature.
Because of this the inventive categories previously restricted to are maintained for purposes of examination.
Claim Status
Claims 1-3, 5, 16-19 & 27-29 are under examination on the merits.
Claims 8, 12 & 20-26 are withdrawn from consideration.
Claims 4, 6-7, 9-11 & 13-15 are canceled.
Priority
Claims 1-3, 5, 16-19 & 27-29 receive the U.S. effective filing date of 12/21/2020.
Previous objection to the specification is withdrawn due to Applicant’s amendment to the specification.
Previous rejection of claims 2-3, 5 & 15-19 under 35 U.S.C. 103 is withdrawn due to Applicant’s response to 105 request and arguments.
Claim Objections
Claim 1 is objected to because of the following informalities:
Amended claim does not reflect the species election restriction (i.e. SEQ ID NO.1 and SEQ ID NO.2) 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 1-3, 5, 16-19, & 27-28 are rejected because the claimed invention is directed to detection or diagnosis of a naturally occurring phenomenon without significantly more. Applicant has amended to recite use of such material ‘for breeding’ but this is so generic as to not add any informative step or limitation to the claims.
Due to Applicant’s amendment of the claims, the rejection is modified from that set forth in the Office action mailed 30 July 2025 as applied to claims 1-3, 5 & 16-19. Applicant’s arguments 2 April 2026 have been considered but are not persuasive.
The claims are drawn to a process, being methods of identifying clubroot-resistant Brassica plants based on the presence of a particular QTL. This QTL comprises linked marker sequences SEQ ID NO.1 & 2.
This is a natural phenomenon (i.e. a product of nature) because the claimed disease resistance and causative QTL(s) is naturally occurring in Brassica rapa, specifically the germplasm population ECD-04. The QTL from ECD-04 confers the phenotypically selectable trait of interest (i.e. clubroot resistance) in the instant application.
The claims do not recite additional elements that amount to significantly more than the judicial exception, as no further steps are included as limitations following the detection or identification (i.e. diagnosis) of disease-resistant plants. Applicant is merely diagnosing the presence or absence of a clubroot resistance allele, which would be conferred by the naturally occurring QTL from ECD-04. Amendment to include language that selected material is used ‘for breeding’ is generic. Broadest reasonable interpretation of plants used ‘for breeding’ would include their use as resistant check varieties in field trials, wherein one merely observes their resistance (i.e. observes the natural phenomenon of resistance due to naturally occurring QTL).
Applicant further recites the use of PCR-based molecular markers in diagnosing/detecting disease resistance, but this use of PCR in molecular diagnosis of naturally occurring genetic variation is now routine, absent evidence to the contrary.
Claims 1-3, 5 & 27-28 recite a method of identifying a plant or part thereof which contains native DNA sequence in the form of a genetic locus (i.e. QTL) conferring disease resistance or susceptibility. Claims are drawn to ‘detection of the QTL’ (claim 1), 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 related to ECD-04 exposed to clubroot through routine field observation and scoring of disease incidence. This would extend to tests designed to determine zygosity of lines (claim 27), such as progeny testing (i.e. by obtaining descendants, claim 28). Additional elements of ‘genotyping’ (claims 2-3 & 5) are added to include molecular diagnosis of ECD-04 resistance allele carriers.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because Applicant does not modify or otherwise include any further inventive steps or modifications beyond detecting the naturally occurring clubroot resistance from turnip germplasm. Applicant is simply performing a diagnosis of natural clubroot resistance conferred by ECD-04 without describing modification of this source of resistance beyond its naturally occurring state.
Claims 16-19 are drawn to individual plants diagnosed with such methods. However, 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.
Applicant has indicated the pedigree or origins of their source of disease resistance, which is a resistant B. rapa plant from the population ECD-04 [Applicant response 2 Apr 2026; p.2, ¶.2, l.1-2 & ¶.3, l.1-4]. The population ECD-04 is a widely used source of clubroot resistance alleles consisting of self-incompatible B. rapa plants [see review by Dixon (2026) The Journal of Horticultural Science and Biotechnology, 101:4, 481-495]. This indicates the QTL at issue, or source of clubroot resistance now claimed, is a naturally occurring sequence in existing germplasm and 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].
Such diagnosis of the phenotype of an organism using naturally occurring alleles, absent further applied steps, lacks integration into a practical application or inventive method. It is merely describing the natural world using phenotypic and/or molecular diagnostic processes.
Because of this, claims 1-3, 5, 16-19 & 27-28 are rejected.
Response to Arguments
Applicant urges that rejection of claims 1-3, 5, & 16-19 under U.S.C. 101 as directed to diagnosis of naturally occurring phenomena is improper because the origin of the resistance is not relevant since claims recite practical application of germplasm [Remarks, p.13, ¶.1-2]. Applicant argues that newly amended claims recite a ‘use in breeding’ which is not an insignificant activity, and thus provides a specific, practical application of the QTL in question [Remarks, p.13, ¶.2-3].
This is not found persuasive because the source of a particular gene, allele, or phenotype is relevant to determination of whether the causative allele is naturally occurring, or is the result of directed mutagenesis, genetic engineering, or other known techniques used to generate allelic and phenotypic diversity beyond that which is naturally occurring.
Applicant’s argument is further unpersuasive because addition of “using the Brassica…for breeding” does not add any specific steps to the claimed invention. Broadest reasonable interpretation of using a plant ‘for breeding’ could encompass nearly any activity involving the reproduction or differential selection of plants, up to and including the general observation of Brassica plants under natural selection forces. The amended claim language is vague and adds no further informative limitation beyond that of diagnosing plants to be used in some broadly generic way.
Applicant is advised to amend and recite a specific breeding step or process which identified plants are to be used in/for that would clarify what breeding method(s) are performed after plants are diagnosed.
Claims 16-19 are rejected because the claimed invention is directed to a plant or plant part containing a naturally occurring allele. The claims recite ‘a plant cell, part, or part thereof, or a seed’ identified or selected by detecting a clubroot resistance QTL, either generally (i.e. claim 1) or via use of DNA markers (i.e. claims 2-3 & 5). This judicial exception is not integrated into a practical application because the disease resistance and its associated DNA sequences of SEQ ID NO.1 & 2 are established as naturally occurring in turnip germplasm, including ECD-04. The limitations of claims 16-19 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they do not recite any novel structural features other than the naturally occurring disease resistance or its causative DNA sequence(s).
Due to Applicant’s amendment of the claims, the rejection is modified from that set forth in the Office action mailed 30 July 2025 as applied to claims 16-19. Applicant’s arguments 2 April 2026 have been considered but are not persuasive.
Applicant states their claimed plants are identified or selected based on resistance to clubroot and comprise a QTL with associated marker sequences SEQ ID NO.1 & 2. Clubroot resistance is known to be naturally occurring and associated with turnip germplasm, more particularly the ECD-04 population [Yang, Abstract].
Applicant has described the disease resistance/QTL in question using an internally coded line ‘Br-14’. Applicant has further indicated the origin of ‘Br-14’ as a resistant B. rapa plant (i.e. a turnip) from the population ECD-04 [Applicant response, p.2, ¶.2-3]. The population ECD-04 is a widely used source of clubroot resistance alleles consisting of self-incompatable B. rapa plants [See Abstract in Yang, and, review by Dixon]. This indicates the QTL at issue, or source of clubroot resistance now claimed (i.e. method of claim 1), is a naturally occurring sequence in existing germplasm and a native, naturally occurring gene/allele. The plants or plant parts resulting from selection of clubroot resistance in ECD-04 or derivatives would reasonably carry this resistance and its causative DNA sequences (i.e. inherent marker sequences).
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]. Applicant’s claimed disease resistance is merely an identification of the native clubroot resistance QTL of ECD-04, which elicits the same plant defensive response(s) as those being described by Yang [p.1503, col.2, ¶.1; p.1505, Figure 2; p.1508, col.2, ¶.1—p.1510, col.1, ¶.3]. Claims 16-19 are directed to this natural phenomenon.
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. In the instant case, the claimed plants comprise just such a naturally occurring allele.
Such claims attempt to possess a naturally occurring gene through its technical description or diagnosis. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they merely claim a naturally occurring allele, described as a QTL, without further inventive steps beyond its inherent properties of disease resistance.
Because the claimed invention is directed to a natural phenomenon, merely being naturally occurring clubroot resistance from ECD-04 and its associated DNA sequence(s), without significantly more, claims 16-19 are rejected.
Response to Arguments
Applicant urges that rejection of claims 16-19 under U.S.C. 101 as being drawn to naturally occurring alleles is improper because the origin of the resistance QTL is not relevant to determining if it is a naturally occurring allele [Remarks, p.13, ¶.1-2]. Applicant further argues that provision for the patenting of eligible plant breeds indicates the claims of the instant invention would be allowable because the claimed products (i.e. the plants possessing the naturally occurring resistance QTL/allele) are produced via methods drawn to marker-assisted selection [Remarks, p.12, ¶.3].
This is not found persuasive because (a) Applicant is not claiming a newly developed plant breed, or specific named cultivar, and (b) a disease resistant plant, that is not a specific plant breed or cultivar claimed, represents a claim to natural genetic variation and/or biodiversity, broadly.
With respect to (a); Applicant’s claims 16-19 are drawn to a product-by-process, namely any plant with a particular disease resistance QTL (i.e. allele) diagnosed. The claims are not limited to a specific cultivar they have developed, or any specific configuration of phenotypic traits or haplotype(s) that would identify a particular breeding line, cultivar, or suite of breeding germplasm beyond that of having what appears to be a single gene/allele underpinning a clubroot resistance phenotype. This resistance allele also appears to be naturally occurring based on Applicant’s admitted source germplasm ECD-04. As such, any Brassica plant having said naturally occurring allele would be encompassed, including the source ECD-04, and these claims are not directed to any specific, definable plant breed (i.e. stable line or cultivar).
With respect to (b); Applicant has not claimed a specific germplasm line or cultivar. Applicant has not claimed the plant ‘Br-14’, and has indicated the source of their resistance QTL/allele is ECD-04 [Applicant response 2 Apr 2026; p.2, ¶.2, l.1-2 & ¶.3, l.1-4]. The ECD-04 population has disease resistance alleles which are unique and have been shown to have natural evolutionary origin in turnips [Yang, p.1508, col.2, ¶.1—p.1510, col.1, ¶.3]. Thus, the clubroot resistant plants or plant parts of claims 16-19 are plants having one of the several naturally occurring disease resistance alleles originating from ECD-04. Moreover, the ECD-04 population itself, if subjected to genetic screening, would predictably be diagnosed or identified as outlined by Applicant. Phenotypic screening of ECD-04 populations or progeny may also preferentially select sequences naturally occurring and associated with this QTL.
For these reasons, and absent the claim of a specifically defined breeding line or cultivar which comprises this naturally occurring allele with additional defining characteristics distinctive of a stable plant breed or cultivar, claims 16-19 remain rejected as drawn to a naturally occurring gene or allele causative of the QTL and observed disease resistance claimed in the instant application.
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, 16 & 28-29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Diedrichsen [Plant Breeding 115, 5—10 (1996); Published 1996].
The claims require a method that (a) identifies a Brassica plant comprising a QTL conferring clubroot resistance, that (b) the disease resistance QTL are detected, and (c) the clubroot resistant plant is used for breeding purposes. Claim 29 requires the additional limitation that a plant comprising the detected resistance is not B. rapa.
Claim 1 does not include a limitation that the identification of the disease-resistant plant requires extraction of DNA or use of specific molecular markers. It only states that one detects a disease-resistant plant carrying the clubroot resistance locus (i.e. comprising its genetic markers). As currently written, the recitation of SEQ ID NO.1 & 2 marker sequences merely indicates the bounds of the target QTL but these are not required in its detection. As such, phenotypic screening of plants would potentially identify or select source plants carrying the locus conferring this resistance, to be used in breeding.
In response to the non-final Office action mailed 13 February 2026 and 105 request/interrogatories, Applicant has indicated the internally coded ‘Br-14’ line used as the source of their resistance QTL is an individual plant from the publicly available ECD-04 population [p.2, ¶.2, l.1-2 & ¶.3, l.1-4].
Diedrichsen describes the breeding a clubroot resistant Brassica plant which carries disease resistance QTLs and is identified by phenotypic screening [p.5, col.2, ¶.2—p.6, col.1, ¶.1; Table 1]. This plant is a progeny of ECD-04 [id]. The population ECD-04 comprises Brassica plants having several inherent genes or loci conferring clubroot resistance. QTL and linked DNA sequences conferring such resistances would inherent to any ECD-04 Brassica plants identified phenotypically from this known, characterized population (i.e. the resistance locus is identical by descent).
Diedrichsen further describes the use of ECD-04, and thus the inherent clubroot resistance QTL, in the breeding of clubroot resistant B. napus resynthesized lines [p.7, col.1, ¶.2; p.8, col.2, ¶.2—p.9, col.2, ¶.1].
Thus, Diedrichsen discloses identification of plants comprising clubroot resistance QTL, which are detected via resistance screening, and used in breeding. They specifically describe this approach using the same Brassica population, ECD-04, as Applicant.
Regarding claim 1; the recited limitations of (a) identifying Brassica plants comprising a QTL for clubroot resistance, (b) detection of disease resistance loci in ECD-04, and (c) using the Brassica plant for breeding are met by Diedrichsen. They clearly disclose identification of clubroot resistant ECD-04 plants, detection of their inherent QTL and/or genetic resistances by phenotypic (i.e. clubroot resistance) screening, and use of resistant ECD-04 plants in further breeding. Because the source germplasm used by Applicant (i.e. the ‘Br-14’ plant from ECD-04) is the same as the clubroot resistance source described by Diedrichsen (i.e. ECD-04) these are the same, absent evidence to the contrary.
Regarding claims 16 & 28; the methods of using ECD-04 in generating disease resistant derivatives or progeny are also disclosed by Diedrichsen who describes crossing ECD-04 to ECD-15 to generate progeny (i.e. seeds and/or descendant plants) carrying clubroot resistance QTL from, and inherent to, ECD-04. [p.5, col.2, ¶.2].
Regarding claim 29; the methods described by Diedrichsen encompass interspecific crosses of ECD-04 and identification of progeny which are not B. rapa (i.e. they are interspecific ‘resynthesized’ or B. napus-like plants) [p.5, col.2, ¶.1].
Because the claimed method merely relies on identification and/or detection of resistant plants comprising QTL and/or clubroot resistances inherent to ECD-04 which can be detected and/or selected via phenotypic disease screening, claim 1 and dependents 16 & 28-29 are rejected. The disclosure of Diedrichsen describes use of ECD-04, specifically for its inherent clubroot resistance QTL and/or genes, and thus anticipates Applicant’s claims. One phenotypically selecting clubroot resistant ECD-04 plants, or their progeny, would reasonably select the genes, DNA sequences, or underlying QTL conferring this resistance including those recited by Applicant, absent evidence to the contrary.
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- 3, 5, 17-19 & 27 are rejected under 35 U.S.C. 103 as being unpatentable over Diedrichsen in view of Mehraj [Plants 2020, 9, 726; Published 9 June 2020].
Diedrichsen teaches the use of B. rapa, and EDC-04 specifically, as a source of clubroot resistance alleles and the selection of clubroot-resistant Brassica progeny from crosses with EDC-04, as outlined above [see p.12, ¶.5—p.14, ¶.2].
Diedrichsen does not teach the use of molecular markers to identify and/or select clubroot resistance QTL in B. rapa.
Mehraj teaches known sources of clubroot resistance and use in developing molecular markers 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. Mehraj goes on to teach the use of that information, development of markers for identifying and selecting improved disease-resistant Brassica [p.9, ¶.1, ‘Resistant Breeding, Gene Accumulation, and MAS].
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to modify the development of clubroot resistant Brassica derived from EDC-04 taught by Diedrichsen to a method employing use of molecular markers to select the causative disease resistance as described in Mehraj.
One of ordinary skill in the art would have been motivated to do so because it was known at the time of filing that EDC-04 was a reliable source of clubroot resistance alleles and applying the known method of developing and using molecular markers to select clubroot resistance in breeding populations utilizing EDC-04 would predictably result in linked markers that would allow more rapid selection of QTL conferring resistance (i.e. no phenotypic screening would be required).
Regarding claims 1-3, 5 & 17-19; claims recite limitations of identifying a Brassica plant and seed having a QTL for resistance to clubroot, doing so via use of DNA and linked molecular markers detected via PCR, and requiring markers of <50cM genetic distance to the QTL. These limitations are met by Diedrichsen who describes identification of clubroot resistance alleles in EDC-04 and development of resistant progeny (claim 1 & 17-19) in combination with Mehraj who describes the marker-assisted selection process of isolation of DNA, identification of linked markers, and selection of plants with clubroot resistance (claims 2-3) [p.4, Figure 2; p.9, ¶.1, ‘Resistant Breeding, Gene Accumulation, and MAS]. While Mehraj does not explicitly state that the markers in question must be within <50cM of the locus of interest, a molecular marker with a genetic distance of 50cM or greater is considered unlinked (i.e. it is not genetically linked to the target). Therefore, any molecular marker used would necessarily be <50cM genetic distance, meeting the limitation introduced by claim 5.
Regarding claim 27; the claim recites the limitation that the zygosity status of the plant is to be determined (i.e. whether it is homozygous or heterozygous) for the target QTL. This limitation is met by Mehraj through the use of molecular markers; doing so would inherently identify plants as either (a) heterozygous or (b) homozygous individuals, thus meeting the limitation introduced by claim 27 of the instant application.
For these reasons, claims 1-3, 5, 17-19 & 27 are rejected as obvious.
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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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
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