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 .
Restriction Requirements
Applicant’s amendment of claims 14 and 42 submitted on 05/04/2026 are acknowledged. Applicant has added claim 43 as new claim. Applicant has cancelled the withdrawn claims 27 and 38 drawn to nonelected invention.
Claims 14 and 42-43 are pending.
Thus claims 12-14 and 42 are examined in this Office Action.
Rejection that are withdrawn
Previous objection to claim 12 has been withdrawn in light of applicant’s cancellation of claim 12.
35 USC § 112 – Indefiniteness rejection has been withdrawn in light of applicant’s cancellation of claim 12 and amendment of claim 42 to recite the phrase “the marker locus”.
35 USC § 102 rejection has been withdrawn in light of applicant’s cancellation of the claim.
35 USC § 112 (a)-Enablement rejection has been withdrawn in light of applicant’s cancellation of claims 12-13.
Claim Objections
Claims 14 and 42 objected to because of the following informalities:
Claim 14, line 5, claim 42, lines 5 and 7-8 recite scientific name “Glycine canescens” which is advised to italicized by convention.
Appropriate correction is required.
Following analysis has been modified in light of applicant’s amendment of claim 14 to delete the recitation of “1cM” genetic distance recited in previous claim set and amendment of claim 42 to delete the recitation of “0.5cM” genetic distance and instead claiming any of the associated ASR resistance allele or favorable allele in an interval to the markers.
Claim Rejections - 35 USC § 112 – Written Description Requirement
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 14 and 42-43 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.
Breadth of the Claim
The association of molecular marker and the one or more ASR resistance allele would encompass any associations (claims 14 and 42).
ASR resistance allele would have any structure (claim 14).
One or more ASR resistance allele in SEQ ID NO:2 associated with one or more SNPs in interval between position 560,975 and 575,551 can have any structure (claim 42).
Any favorable allele in SEQ ID NO:2 in interval between position 560,975 and 575,551 can have any structure (claim 42).
What is Described in the Specification
Applicant describes the following:
A resistant parent was crossed to a susceptible G. canescens line and an F1 plant was generated (see Table 4) (page 333, lines 4-5).
Around 200 F2 seed were sown and leaf tissue from each plant was collected for DNA preps and then the plants were inoculated with Phakopsora pachyrhizi to determine the resistance/susceptible phenotype of each F2 individual (page 333, lines 6-8).
Around 1000 SNPs were found to have possible linkage to the target locus wherein A subset of these putatively linked SNPs was used to fine map the locus using phenotyped F2 individuals (page 333, lines 29-31).
In soybean population from line PI595799 the clustering of SNPs indicates that the resistance gene is located on or near scaffold 000090F (SEQ ID NO: 2) (page 334, lines 24-27).
The context sequences associated with these SNPs were also aligned to the public G. max genome to create a chromosome-level understanding of the mapping interval (page 334, lines 27-29).
wherein the chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2, 442, 980 of SEQ ID NO: 2 (page 324, lines 1-4).
Scaffold 000090F has been mapped to G. canescens chromosome 14 wherein SEQ ID NO. 2 is a chromosomal interval derived from Glycine canescens line accession PI595799 from the "Scaffold 000090F" (page3, lines 20-23).
Tables 1-3 were determined to be significantly linked with resistance or susceptibility (p<0.05) (page3, lines 31-33).
Difference Between What was Described and What is Claimed
Applicant has not described the association of molecular marker and the ASR resistance allele other than a genetic linkage between the molecular marker and the ASR resistance allele.
Applicant has not described ASR resistance allele comprises T at a position corresponding to position 570, 525 of SEQ ID NO: 2, since the structure of ASR allele is not known.
Applicant has not described the association of ASR resistance allele with a T at a position corresponding to position 570,525 (claim 14) and association of any of the ASR resistance alleles or any favorable alleles between and including C at position 560,975 and an A at position 575,551 of SEQ ID NO· 2 (claim 42) in any other plant other than PI595799.
Analysis
The purpose of the written description is to ensure that the inventor had possession at the time the invention was made, of the specific subject claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
Applicant has not described marker locus comprises Glycine canescens ASR resistance allele. Applicant describes the marker “T” is significantly linked to resistance at P<0.05 (Spec, page 3, lines 30-33 and Table 2) among the large number of markers with very wide peaks of significance ranging several megabases (see Table 2) without validation. Applicant defines in specification “As used herein, the terms "marker" and "genetic marker" are used interchangeably to refer to a nucleotide and/or a nucleotide sequence that has been associated with a phenotype, trait or trait form (page 318, lines 1-3).” And “As used herein, the terms "molecular marker" or "genetic marker" may be used to refer to a genetic marker, as defined above, or an encoded product thereof (e.g., a protein) used as a point of reference when identifying a linked locus (page 319, lines 16-18).” For this since the marker are point of reference for identifying a linked locus, there is no indication in specification that the marker locus comprises the Glycine canescens ASR resistance allele associated with increased ASR resistance, instead it is only described as it is linked to the ASR resistance allele and a chromosomal segment would comprise the Glycine canescens ASR resistance allele associated with increased ASR resistance.
Applicant has not described the association of molecular marker and the ASR resistance allele other than a genetic linkage between the molecular marker and the ASR resistance allele. The recitation of term “associates” in claim 14 would mean any kind of association for example Merriam Webster dictionary (https://www.merriam-webster.com/dictionary/associate, accessed 05/01/2025) defines “associates” as to “join or connect together” or “bring together”. Thus, the molecular marker that associates with ASR allele would be joined, connected or be together by any way for example physically, functionally, or being in any networks of functions. Applicant does not claim the necessary (i.e., favorable) allele(s) associated with the particular SNP markers, such that, Applicants do not disclose a conserved structure responsible with respect to the markers and alleles as to accomplish the instantly claimed function of ASR resistance phenotype in soybean.
Applicant states the “A marker is "associated with" a trait when it is linked to it and when the presence of the marker is an indicator of whether and/or to what extent the desired trait or trait form will occur in a plant/germplasm comprising the marker. Similarly, a marker is "associated with" an allele when it is linked to it and when the presence of the marker is an indicator of whether the allele is present in a plant/germplasm comprising the marker” (Spec, pages 313 and 314, lines 31-35 and 1-2). Furthermore, applicant defines “As used herein, the term "linkage" refers to the degree with which one marker locus is associated with another marker locus or some other locus (for example, an ASR tolerance locus). For example, in some embodiments, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM).” (Spec, page 316, lines 30-35). Therefore it is clear that the recitation of "associated with" would not limit the linkage to specific centimorgans or it only states that the marker is indicator of trait is present in the plant/germplasm genome. Therefore it is not clear without reciting the germplasm PI595799 that the specific polymorphism in SEQ ID NO:2 and associated alleles would be found (page3 , lines 21-23) therefore a skilled in the art would not determine the association between a corresponding sequence and a ASR resistance allele without the association found in germplasm PI595799. Therefore there is dearth of description of the association of molecular marker and the ASR resistance allele other than a genetic linkage between the molecular marker and the ASR resistance allele.
The claims are drawn to any unspecified marker of any marker type, as long as the marker is associated with a ASR resistance allele. The claims are not limited to alleles with the SNP indicative of the claimed phenotype of ASR resistance in soybean. Instead, applicant has not described the association of molecular marker and the ASR resistance allele other than a genetic linkage between the molecular marker and the ASR resistance allele. Thus, there is dearth of description of any association of molecular marker and the ASR resistance allele.
Lee et al. (Year: 2020, Journal: Genomics 112(2): 1481-1489) teaches in soybean, the average recombination rate for each chromosome ranges from 1.9 to 3.4 cM/Mb with a genome-wide average of 2.5 cM/Mb. Lee et al. teaches approximately 170 marker intervals with recombination rates higher than 20 cM/Mb have been reported. Suggesting that although a genetic map may provide an overall structure of chromosomes, a reliable for example 100-kb resolution would not be achieved for large parts of chromosomes even with a map density of 0.1-cM marker interval (page 1482, left paragraph 2).
Furthermore, for example applicant states in 150 backcross plants, there is a 95% chance that at least one plant will have experienced a crossover within 1 cM of the gene, based on a single meiosis map distance (page 322, lines 33-35). With one additional backcross of 300 plants, there would be a 95% chance of a crossover within 1 cM single meiosis map distance of the other side of the gene, generating a segment around the target gene of less than 2 cM based on a single meiosis map distance (page 322, lines 35-36, page 323, lines 1-2). Applicant states for example, in smaller population sizes, recombination may be expected further away from the gene, so more distal flanking markers would be required to detect the recombination (page 323, lines 5-6). Applicant states a number of SNP alleles together within a sequence, or across linked sequences, can be used to describe a haplotype for any particular genotype. Ching et al., BMC Genet. 3:19 (2002); Gupta et al., (2001), Rafalski, Plant Sci. 162:329 (2002b). Haplotypes can be more informative than single SNPs and can be more descriptive of any particular genotype. Applicant teaches for example, a single SNP may be allele "T" for a specific Disease resistant line or variety, but the allele "T" might also occur in the soybean breeding population being utilized for recurrent parents. In this case, a combination of alleles as linked SNPs may be more informative. Once a unique haplotype has been assigned to a donor chromosomal region, that haplotype can be used in that population or any subset thereof to determine whether an individual has a particular gene (page 323, lines 24-30).
For this reason, the recitation of combination of significant SNPs or haplotypes, or reference to specific marker loci sequences linked to resistance in the SEQ ID NO:2 would be more determinant of whether an individual soybean plant would have a particular ASR gene described by applicant.
Instead, applicant has not described any method of detecting marker “T” corresponding to position 570,525 of SEQ ID NO: 2 near an ASR resistance allele from G. canescens other than the marker “T” is significantly linked to resistance at P<0.05 (Spec, page 3, lines 30-33 and Table 2) among the large number of markers with very wide peaks of significance ranging several megabases (see Table 2). This would be problematic since it does not clearly show the expected mapping resolution to show that the locus is within 1cM from the ASR resistance allele. The resolutions is further unclear because such wide peaks of significance ranging several megabases is produced in a small Bulk segreant population comprising 50 resistant F2s and 50 susceptible F2s (page 333, lines 1-14). For example, Lee et al. teaches mapping resolution is limited by mapping population size (page 1487, right last paragraph). For this reason, there is dearth of description of detecting a ASR resistance allele located within 1cM of the “T” at position 570, 525 of SEQ ID NO: 2.
Applicant has not described ASR resistance allele comprises “T” at a position corresponding to position 570, 525 of SEQ ID NO: 2, since the structure of ASR allele is not known. Applicant has only described ASR resistance allele with its linkage to the molecular maker comprising “T” corresponding to position 570, 525 of SEQ ID NO: 2. Nowhere in specification applicant describes ASR resistance allele comprises T at a position corresponding to position 570, 525 of SEQ ID NO: 2, since the structure of the ASR resistance allele has not been described and its only described by linkage relation with the molecular marker locus. Therefore, there is dearth of description of ASR resistance allele comprises “T” at a position corresponding to position 570, 525 of SEQ ID NO: 2 since the ASR allele has only been described by its linkage to the molecular marker.
Accordingly, the claims are drawn to an extremely broad method of selecting soybean plant that would require to locate a ASR resistance allele within 1cM of the polymorphism “T” at position 570, 525 of SEQ ID NO: 2, which is an approximate genetic distance measured by 1% chance of recombination during meiosis. Furthermore, since the recombination is determined by many factors including a location of the marker and gene, or by number of segregating progenies screened for mapping, the distance of 1cM in a chromosome could mean any physical distance. The claims are drawn to any unspecified marker of any type and sequence, and any unspecified allele, vs. the exemplified SNPs listed in the Specification.
The chromosomal interval corresponding to SEQ ID NO:2 recited in claim 42 would encompass large interval since interval including and located between a C at position 560, 975 and an A at position 575,551 of SEQ ID NO: 2 (claim 42) encompass ~14,576 bp which would encompass many favorable alleles or ASR resistance alleles. Applicant states SEQ ID NO. 2 is a chromosomal interval derived from Glycine canescens line accession PI595799 referred to herein as "Scaffold 000090F" which is 1, 966, 948 (i.e. ~2Mb) nucleotides long, Scaffold 000090F has been mapped to G. canescens chromosome 14 (page3, lines 21-23). Therefore, there is dearth of description of associated one or more ASR resistance allele, and any favorable allele located between C at position 560, 975 and an A at position 575,551 of SEQ ID NO: 2 (claim 42) from G. canescens plant that would increase resistance to ASR when provided to G. max plant (claim 12).
Furthermore, Applicant has not described SEQ ID NO:2 is found in any other plant other than PI595799. The line is required to find the association of the corresponding position of T, C, and A’s recited in claims 14 and 42 in SEQ ID NO:2, since marker would only show the linkage relation between a gene and marker, and does not describe where the ASR resistance allele or any favorable allele is located without comparison of the linkage relation or association of the marker with the resistance or favorable allele in the line PI595799. Furthermore, it is not clear how far are the ASR resistance allele from the SNPs in the recited interval of C at position 560, 975 and an A at position 575,551 of SEQ ID NO: 2 since a molecular marker would only indicate the presence of allele in the genome and does not clearly show how far and which are the alleles associated with the recited markers. Applicant describes SEQ ID NO. 2 is a chromosomal interval derived from Glycine canescens line accession PI595799 referred to herein as "Scaffold 000090F" which is 1, 966, 948 (i.e. ~2Mb) nucleotides long, and Scaffold 000090F has been mapped to G. canescens chromosome 14 (page 3, lines 21-23). Applicant described the other G. canscens lines Pl440935 and Pl483193 comprise different sequences of SEQ ID NO:1 and 3 respectively (page 3, lines 19-33). Therefore, there is dearth of description of SEQ ID NO:2 is found in any other plant other than PI595799 that would have alleles to increase the ASR resistance in G. max.
Relating to structure vs. function, the claims remain drawn to any unspecified ASR alleles or any favorable alleles, this leads to a situation where the instantly claimed allele of the claimed ASR loci would not possess the necessary structural features needed to accomplish the claimed phenotype. The Specification makes clear that the specific single nucleotide polymorphisms comprised within the marker alleles lend to the phenotype corresponding to specific line PI595799, thus it is necessary to claim the polymorphisms as such (i.e., specific favorable alleles).
Given Applicants have provided very vague description of the method steps or structures that would link a myriad of unspecified ASR resistance alleles that have any form of association with the any SNPs or SNPs T at a position 570,525 corresponding to SEQ ID NO:2 (claim 14), and SNPs between and including C at position 560, 975 and an A at position 575,551 of SEQ ID NO· 2 (claim 42), and the alleles are determinants of ASR resistance in soybean, it remains unclear what features or method steps are capable of performing the claimed function. Applicant has showed about 133 specific SNPs between position 560, 975 and position 575,551 (Spec, pages 140-142). Applicant has not described whether the SNPs are associated with one or more ASR resistance allele or any favorable alleles. Since association does not mean close linkage or physical proximity of alleles and the SNPs the association would have only been corresponding to genome of the line PI595799. Without the reference to line PI595799, one skilled in the art would not find the association between any of the ASR resistance alleles, or any favorable alleles in or corresponding to SEQ ID NO: 2. encompassed by the claim. Thus, the Specification fails to provide an adequate written description to support the breadth of the claims. Therefore, one skilled in the art would not have recognized Applicants to be in possession of the claimed invention at the time the application was filed.
Lee et al. further showed even if the genome-wide average recombination rate is considered in the soybean plant, any marker that is farther than 3.4 cM would be in completely different place than the gene because the recombination would lead to the method not detecting the marker gene association. For this reason, the recitation of combination of SNPs or haplotypes, or reference to specific marker loci sequences linked to resistance in the SEQ ID NO:2 within the average recombination would be more determinant of whether an individual soybean plant would have a particular gene.
Applicant has not described providing as crossing the any Glycine canescens plant line would result in viable seeds to regenerate (claim 12). Singh et al. teaches the attempts to cross a hybrid between the wild perennial species G. canescens with domestic G. max results in sterile plants (col. 4, lines 30-33, lines 59-61, col. 5, lines 15-18). Therefore, it is not clear whether providing chromosomes from G. canescens would be able to pair with G. max to produce seeds for regeneration in any of the G. canescens x G. max hybrids. Instead, applicant has only described crossing lines of G. canescens to transfer the ASR genes (page 334, Table 4). Therefore, there is dearth of description of producing seeds for regeneration in any of the G. canescens x G. max hybrids by virtue of examples.
"The test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to one skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad Pharm, Inc, v EH Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Lockwood v. Amer. Airlines, ina, 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). "An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations. Lockwood, 107 F.3d at 1572, 41 USPG2d at 1966". While the written description requirement does not demand either examples or an actual reduction, actual "possession" or reduction to practice outside of the specification is not enough. Ariad Pharm, Inc. v. Eli Lilly & Co., 598 F,3d 1336,1352 (Fed. Cir. 2010). Rather, it is the specification itself that must demonstrate possession. Id.
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. As a result, it is not clear that Applicant was has described the structure of claimed genus to have application as recited function at the time this application was filed.
Response to Argument for Rejection
Applicant's arguments 05/04/2026 have been fully considered but they are not persuasive.
Applicant argues one of skill in the art, such as a plant breeder or geneticist, would be familiar with marker assisted selection wherein molecular markers are used to select desired traits they are associated with. Applicant argues the definition of association between a marker and the trait it is linked to is provided in Applicant's specification as filed at page 313, line 31 - page 314, line 2 (paragraph [0042] of the instant US patent publication No. US20220256795). Applicant argues references related to Marker Assisted Breeding are also disclosed in Applicant's specification at page 314, lines 7-11 (paragraph [0043] of US patent publication No. US20220256795). Applicant argues as indicated in the specification and the disclosed references, one of skill in the art would recognize that a marker is associated with an allele when the presence of the marker is an indicator of the presence of the allele in the plant/germplasm comprising the marker. Applicant argues in Applicant's claims, the recited markers and the favorable alleles associated with them are indicated as being located on the chromosomal interval of SEQ ID NO: 2, which is responsible for conferring ASR resistance (Response to rejection, page 5, paragraph 3).
Applicant states Applicant has amended claim 42 to independent form reciting a method of selecting comprising assaying for the presence of multiple favorable alleles located between, and including, a C at position 560,975 and an A at position 575,551 of SEQ ID NO: 2. Applicant states these alleles are located around the allele at position 570,525 of SEQ ID NO: 2. Applicant submits that an identity of the causative gene derived from the chromosomal interval of SEQ ID NO: 2 that is responsible for conferring ASR resistance is disclosed in co-pending application US 17/631, 174 (published as Patent Pub. No. US20220267789).
Regarding argument on definition of “associated” in pages 313-314, the argument was not found persuasive since Applicant states (without “as used herein”) the “A marker is "associated with" a trait when it is linked to it and when the presence of the marker is an indicator of whether and/or to what extent the desired trait or trait form will occur in a plant/germplasm comprising the marker. Similarly, a marker is "associated with" an allele when it is linked to it and when the presence of the marker is an indicator of whether the allele is present in a plant/germplasm comprising the marker (Spec, pages 313 and 314, lines 31-35 and 1-2). Furthermore, applicant defines “As used herein, the term "linkage" refers to the degree with which one marker locus is associated with another marker locus or some other locus (for example, an ASR tolerance locus). For example, in some embodiments, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM).” (Spec, page 316, lines 30-35). Therefore, it is clear that the recitation of "associated with" would not limit the linkage to specific centimorgans or it only states that the marker is indicator of trait is present in the plant/germplasm genome. Therefore without reciting the germplasm PI595799 in claims (page3 , lines 21-23), a skilled in the art would not determine the nature of association between a corresponding sequence and a ASR resistance allele. Therefore, there is dearth of description of the association of molecular marker and the ASR resistance allele other than a genetic linkage between the molecular marker and the ASR resistance allele.
Regarding argument on co-pending application US 17/631, 174, the argument was not found persuasive since applicant has not described how long is the genetic or physical distance between resistance gene recited in copending application US 17/631, 174 from the recited SNPs in the instant claims. The alignment of sequence for example SEQ ID NO: 2 with the sequence of the copending application does not provide clear indication of associations between SNPs and the gene. Furthermore, claim 42 recite unknown number of ASR allele associated with the SNPs between and including the position 560, 975 and 575,551bp. Therefore, there is dearth of description of association between SNPs and one or more ASR resistance allele. Therefore, the rejection has been maintained.
Summary
No claim is allowed.
Claims 14 and 42-43 are free of prior art. The closest art is Burdon et al. (Year: 1988, Journal: Theoretical and Applied Genetics, 75, 923-928) (Cited and included in previous office action) which teaches analysis of genetic basis of resistance to the soybean rust pathogen Phakopsora pachyrhizi in a set of differential lines of the wild plant G. canescens showed that Asian soybean rust resistance caused by pathogen P. pachyrhizi was dominant and controlled by genes with major phenotypic effects (page 923, Abstract). The patentable distinction is that the Burdon et al. does not teach their method comprise their resistance allele is located within chromosomal interval comprising SEQ ID NO:2 and the resistance allele comprises a T at a position corresponding to position 570,525 of SEQ ID NO: 2 (claim 14) or the ASR alleles associated with SNPs between and including C at position 560, 975 and an A at position 575,551 of SEQ ID NO: 2 (claim 42).
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663
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