DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 10/29/2025 has been entered.
Claim Status
Claims 1-26 remain pending.
Claims 10-18 remain withdrawn as being drawn to an unelected invention.
Claims 1, 2, 5-7, 19-21 and 23-24 are newly amended.
Claims 1-9 and 19-26 are examined on the merits.
Claim Objections
Claim 1 is newly objected to because of the following informalities: the claim recites “a traited version of a target line” and also recites “traited progeny population” and “traited target line”. These later recitations should be amended to recite “a traited version of a target line” or similar language in order to maintain consistency. Alternatively if these terms are used intentionally then indefiniteness rejections may be required as the exact scope of a “traited version of a target line” is unclear given the context in the claim.
Appropriate correction is required.
Claims 5 and 23 are newly objected to because of the following informalities: the claims each recite “the traited target line”. In order to use consistent language the office suggests changing this to “the traited version of a target line” which is used in independent claim 1. Alternatively if these terms are used intentionally then indefiniteness rejections may be required as the exact scope of imparted to the claim by the use of these terms is unclear given the context in the claim.
Appropriate correction is required.
Claim 19 is newly objected to because of the following informalities: the claim recites “a genetically modified version of a target line” and also recites “genetically modified progeny population” and “genetically modified target line”. These later recitations should be amended to recite “a genetically modified version of a target line” or similar language in order to maintain consistency. If these terms are used intentionally then indefiniteness rejections may be required as the exact scope is unclear given the context in the claim.
Appropriate correction is required.
Claims 20 and 26 are newly objected to because of the following informalities: the claims recite “the at least one genetically modified target line” and “the genetically modified target line”, respectively. In order to use consistent language the office suggests changing this to “the at least one genetically modified version of a target line”. If these terms are used intentionally then indefiniteness rejections may be required as the exact scope is unclear given the context in the claim.
Appropriate correction is required.
Claims 22 and 25 are newly objected to because of the following informalities: the claims each recite “wherein after step c) a size of the traited progeny population” which should be changed to “wherein after step) the size of the traited progeny population” in order to improve syntax.
Appropriate correction is requested.
Claims 23 and 26 are newly objected to under 37 CFR 1.75 as being substantial duplicates of claims 5 and 20, respectively, given that claims 5 and 20 are drawn to the method of claims 1 and 19, respectively, further comprising crossing the at least one genetically modified target line with the inbred target line. While claims 23 and 26 are drawn to the method of claims 1 and 19, respectively, further comprising performing an additional cross between the genetically modified target line and the inbred target line. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 112 (Indefiniteness)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9 and 19-26 are newly rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
In claims 1 and 19 the recitation of “wherein the traited target line is obtained without the need for multiple generations of inbreeding” renders the claim indefinite. This phrase is in conflict with the following statement from lines 2-5 of step b of claims 1 and 19 which read as follows: “wherein said version was produced by crossing the first parent or second parent with a donor parent comprising said trait of interest followed by backcrossing with said first parent or second parent as the recurrent parent to recover the version”.
That quotation describes methods to introduce a specific trait of interest into the parents of the traited version of a target line and the claim explicitly recites the use of backcrossing in order to recover the version. This appears to mean that backcrossing is used to recover many of the traits of the original parent. As such the claimed method appears to differ from traditional breeding methods only by eliminating a backcrossing step after making the cross of interest but appears to still rely on backcrossing methods to introduce traits of interest into the parent lines.
Figure 10 adds clarity, this figure compares standard trait introgression methods with a traited parent method. The major difference appears to be that the current trait introgression method relies on inbreeding after the initial cross in order to produce the desired line, in this example these inbreeding steps are shown as four backcross steps making clear that backcrossing is considered inbreeding.
As such the scope of “obtained without the need for multiple generations of inbreeding” is not clear because it appears that at some points in the method that inbreeding steps remain necessary, specifically, backcrossing (a step used for inbreeding as demonstrated in figure 10) is used to add the trait of interest to the parent lines, while at others it is not necessary. However, it is not clear at which point in the method inbreeding is not necessary, nor is it clear if methods which use inbreeding are included and if so how to determine if an inbreeding step is needed or not.
As such it is not clear how to tell if an inbreeding step is necessary, it is not clear when inbreeding steps are allowed to be included in the claim and when they are not and as such the scope of the claim is not clear and claims 1 and 19 are rejected as indefinite.
All dependent claims are included for depending on an indefinite claim and failing to limit the claim scope to definite subject matter.
In claims 23 and 26 the recitation of “performing an additional cross between the modified target line and the inbred target line” renders the claims indefinite. This is indefinite because claim 23 depends on claim 1 and claim 26 depends on claim 19 which each do not include a step of performing a cross between the genetically modified target line and the inbred line. Therefore it is not clear whether “an additional cross” refers to another cross in addition to the crosses recited in claims 1 and 19 or whether “an additional cross between the genetically modified target line and the inbred target line” means that the methods of claims 23 and 26 require multiple rounds of crosses between the genetically modified target line and the inbred target line. As such this phrase introduces more than one scope of the claim and claims 23 and 26 are rejected as indefinite.
Response to Applicant Arguments – Anticipation
In response to applicant’s amendments to the claims and arguments dated 10/29/2025 the anticipation rejections of record are withdrawn. Applicant’s amendment of the claims necessitates new obviousness rejections.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 5-6, 8-9, 19-20, 23 and 26 are newly rejected under 35 U.S.C. 103 as being unpatentable over Wardyn, US 11,399,490 B1, filed 10/12/2020.
Claim 1 is drawn to a method of generating a traited version of a target line requiring the following steps:
Providing a target inbred line having a first parent and a second parent.
Providing a version of at least one of the first parent and the second parent that carries at least one trait of interest produced by backcrossing that parent with a suitably donor parent.
Crossing the first parent or said version thereof with the second parent or said version thereof, wherein at least one of the parents in said crossing is the version of the first parent or the second parent.
Selecting a progeny plant having some unknown level or aspect of genetic similarity to the target inbred line.
With respect to claim 1, Wardyn teaches Maize Inbred PH4CF1 and plants produced from Maize Inbred PH4CF1 (Wardyn, Abstract; Wardyn, Column 32, Lines 24-43).
Inbred Target Line = a homozygous PH4CF1 Progeny Plant (Column 34 line 55)
Parent X for Inbred Target Line = PH4CF1 (Column 34 line 57)
Parent Y for Inbred Target Line = Second plant (Column 34 line 57)
Modification of Parent X and Y= PH4CF1 can have an added trait (Column 2 lines 3-16)
Traited Version of the inbred target line = Altered PH4CF1 with the added trait
Wardyn also teaches an inbred homozygous PH4CF1 plant that is substantially similar to PH4CF1 produced by crossing PH4CF1 and another plant and then using doubled haploid methods to the F1 seed to produce an inbred with genetics and characteristics similar to PH4CF1 (Wardyn, Colum 34, Lines 54-64). Wardyn also teaches plants produced by these methods which have the exact same marker profile as maize variety PH4CF1 and demonstrate essentially the same morphological characteristics as maize variety PH4CF1 when grown in the same environmental conditions (Wardyn, Column 34, Line 64-Column 35, Line 5; Wardyn, Column 35, Lines 19-27).
As such Wardyn teaches an inbred line produced from a cross between two parents which has essentially all of the characteristics of maize variety PH4CF1.
Warden also teaches other PH4CF1 inbred plants further comprising an additional trait (Wardyn, Column 2, Lines 3-20). In that same column, Wardyn teaches that the added trait may be conferred by a transgene (Wardyn, Column 2, Lines 14-18). Wardyn also teaches that these traits can be added to PH4CF1 by backcrossing methods (Wardyn, Column 2, Lines 14-18). Further, Wardyn, then teaches that producing PH4CF1 comprising added traits can use double haploid production and that a PH4CF1 plant comprising a transgene (additional trait) can be crossed with a different maize plant (Wardyn, Column 23, Lines 31-55).
As such Wardyn, teaches homozygous inbred lines produced using backcrossing to produce a version of PH4CF1 and further that this plant can be outcrossed to produce F1 plants from which doubled haploid methods can be used to produce an inbred line comprises all of the traits of PH4CF1 and further comprises an additional trait.
With respect to claim 1, Wardyn does not explicitly teach all of the limitations of the claimed invention in a single embodiment.
Given that Wardyn teaches an inbred line produced from a cross between maize inbred PH4CF1 and another line and which is genetically identical to PH4CF1 (the homozygous inbred line is substantially similar to PH4CF1 and shares the exact molecular marker profile with PH4CF1) and further that Wardyn teaches PH4CF1 plants produced using backcross breeding to introgress a transgene carrying a trait into the parent and then doubled haploid methods which rapidly produce a homozygous inbred line comprising the transgene conferring an added trait, it would have been obvious to arrive at the claimed method.
It would have been obvious to arrive at this claimed method because Wardyn in separate embodiments teaches all of the essential structures and steps. Specifically, because Wardyn teaches the two plants described above it would have been obvious to arrive at the claimed method because this would only require the addition of a step of selecting the line comprising the added trait based on genetic similarity between that line and the inbred line that is genetically identical to PH4CF1. This selecting step is implied in producing the PH4CF1 plant comprising the added trait because producing this plant requires selecting for plants which are similar to PH4CF1 (and thereby the inbred homozygous line produced using doubled haploid methods which is genetically identical to PH4CF1).
Claim 1 is rejected as obvious under Wardyn.
With respect to claim 5, Wardyn teaches all of the limitations of claim 1, see above.
With respect to claim 6, Wardyn teaches all of the limitations of claim 1, see above.
With respect to claims 8-9, Wardyn teaches all of the limitations of claim 1, see above.
Further, Wardyn teaches that the added trait can be an agronomic trait such as yield or dry down (Wardyn, Column 21, Lines 4-8).
With respect to claim 23, Wardyn teaches all of the limitations of claim 1, see above.
With respect to claims 5-6, 8-9 and 23, Wardyn does not teach making an additional cross between the traited target line and the inbred target line.
At the time of filing it would have been obvious to modify the method of Wardyn to perform an additional cross between the traited target line and the inbred target line in order to fix the trait in the line and to ensure the utmost genetic identity to parent line PH4CF1. This is because a backcross or cross to a line which is identical to the parent line is a common step to ensure high levels of homozygosity which is standard practice in producing elite inbred lines. The ordinary artisan would have been motivated to perform this additional cross in order to ensure high levels of homozygosity and produce an elite inbred line comprising and additional trait.
As such claims 5-6, 8-9 and 23 are rejected as obvious under Wardyn.
With respect to claim 19, Wardyn teaches Maize Inbred PH4CF1 and plants produced from Maize Inbred PH4CF1 (Wardyn, Abstract; Wardyn, Column 32, Lines 24-43).
Wardyn also teaches an inbred homozygous PH4CF1 plant that is substantially similar to PH4CF1 produced by crossing PH4CF1 and another plant and then using doubled haploid methods to the F1 seed to produce an inbred with genetics and characteristics similar to PH4CF1 (Wardyn, Colum 34, Lines 54-64). Wardyn also teaches plants produced by these methods which have the exact same marker profile as maize variety PH4CF1 and demonstrate essentially the same morphological characteristics as maize variety PH4CF1 when grown in the same environmental conditions (Wardyn, Column 34, Line 64-Column 35, Line 5; Wardyn, Column 35, Lines 19-27).
As such Wardyn teaches an inbred line produced from a cross between two parents which has essentially all of the characteristics of maize variety PH4CF1.
Warden also teaches other PH4CF1 inbred plants further comprising an additional trait (Wardyn, Column 2, Lines 3-20). In that same column, Wardyn teaches that the added trait may be conferred by a transgene (Wardyn, Column 2, Lines 14-18). Wardyn also teaches that these traits can be added to PH4CF1 by backcrossing methods (Wardyn, Column 2, Lines 14-18). Further, Wardyn, then teaches that producing PH4CF1 comprising added traits can use double haploid production and that a PH4CF1 plant comprising a transgene (additional trait) can be crossed with a different maize plant (Wardyn, Column 23, Lines 31-55).
As such Wardyn, teaches homozygous inbred lines produced using backcrossing to produce a version of PH4CF1 and further that this plant can be outcrossed to produce F1 plants from which doubled haploid methods can be used to produce an inbred line comprises all of the traits of PH4CF1 and further comprises an additional trait.
With respect to claim 19, Wardyn does not explicitly teach all of the limitations of the claimed invention in a single embodiment.
Given that Wardyn teaches an inbred line produced from a cross between maize inbred PH4CF1 and another line and which is genetically identical to PH4CF1 (the homozygous inbred line is substantially similar to PH4CF1 and shares the exact molecular marker profile with PH4CF1) and further that Wardyn teaches PH4CF1 plants produced using backcross breeding to introgress a transgene carrying a trait into the parent and then doubled haploid methods which rapidly produce a homozygous inbred line comprising the transgene conferring an added trait, it would have been obvious to arrive at the claimed method.
It would have been obvious to arrive at this claimed method because Wardyn in separate embodiments teaches all of the essential structures and steps. Specifically, because Wardyn teaches the two plants described above it would have been obvious to arrive at the claimed method because this would only require the addition of a step of selecting the line comprising the added trait based on genetic similarity between that line and the inbred line that is genetically identical to PH4CF1. This selecting step is implied in producing the PH4CF1 plant comprising the added trait because producing this plant requires selecting for plants which are similar to PH4CF1 (and thereby the inbred homozygous line produced using doubled haploid methods which is genetically identical to PH4CF1).
Claim 19 is rejected as obvious under Wardyn.
With respect to claim 20, Wardyn teaches all of the limitations of claim 19, see above.
With respect to claim 26, Wardyn teaches all of the limitations of claim 19, see above.
With respect to claims 20 and 26, Wardyn does not teach an additional step of crossing the genetically modified target line with the inbred target line.
At the time of filing it would have been obvious to modify the method of Wardyn to perform an additional cross between the traited target line and the inbred target line in order to fix the trait in the line and to ensure the utmost genetic identity to parent line PH4CF1. This is because a backcross or cross to a line which is identical to the parent line is a common step to ensure high levels of homozygosity which is standard practice in producing elite inbred lines. The ordinary artisan would have been motivated to perform this additional cross in order to ensure high levels of homozygosity and produce an elite inbred line comprising and additional trait.
Claims 20 and 26 are rejected as obvious under Warden.
Claims 2-4, 7, 21-22 and 24-25 are newly rejected under 35 U.S.C. 103 as being unpatentable over Wardyn, in view of Smith.
With respect to claim 21, Wardyn teaches all of the limitations of claim 1, see above.
With respect to claim 2, Wardyn teaches all of the limitations of claim 21 taught above, see above.
With respect to claim 3, Wardyn teaches all of the limitations of claim 2 taught above, see above.
With respect to claim 4, Wardyn teaches all of the limitations of claim 3 taught above, see above.
With respect to claim 7, Wardyn teaches all of the limitations of claim 1, see above.
With respect to claim 22, Wardyn teaches all of the limitations of claim 21 taught above, see above.
With respect to claim 24, Wardyn teaches all of the limitations of claim 19, see above.
With respect to claim 25, Wardyn teaches all of the limitations of claim 24 taught above, see above.
With respect to claims 2-4, 7, 21-22 and 24-25 Wardyn does not teach, steps of estimating a traited progeny population size based on genetic information of the parents and target line (claims 21 and 24), where the size of the traited progeny population is equal to or greater than the traited progeny population size (claims 22 and 25), wherein the estimating a traited population comprises generating virtual genomes by simulating recombination of the parent genomes, estimating similarity between the virtual genomes and the inbred target line comparing these against a similarity threshold, determining a proportion of the virtual genomes that have a similarity that exceeds the similarity threshold, and estimating a probability of a recombination between the parents generating a line whose similarity to the targe line is equal to or exceeds the similarity threshold (claim 2), the method of claim 2 wherein estimating similarity is based on an identity-by-descent method (claim 3), the method of claim 3, wherein the identity-by-descent is a haploid-based identity-by-descent method (claim 4), and wherein the inbred target line of claim 1 is an inbred rapeseed line (claim 7).
With respect to claims 2-4, 7, 21-22 and 24-25 Smith discloses using association analysis generated through the use of the Likelihood ratio TDT Test to predict the number of offspring from a cross which would inherit a trait of interest (white cob color) using association analysis through the use of the Likelihood ration TDT Test (Smith, Page 19, Paragraph 0204; Smith Page 20, Paragraph 0210).
This analysis uses haplotype genetic data from the parent population to identify the target genotype by identifying an association between a marker and a trait of interest (Smith, Page 19, Paragraph 0202; Smith, Page 19, Paragraph 0204; Smith Page 20, Paragraph 0210). This is particularly relevant to claim 21.
Further, as it relates to claim 2, Smith teaches estimating a traited progeny population size comprising the following steps:
Generating a set of virtual genomes by simulating recombination of the genomes of the first and second parent. Specifically, Smith discloses recombining the genomes of a first and second inbred parent to produce a breeding population (Smith, Page 19, Paragraph 0202) which can be done using hypothetical plants (Smith, Page 10, Paragraph 0098). Therefore, the hypothetical recombination of genomes of two parent plants of Smith is the same thing as generating a set of virtual genomes by simulating the recombination between parents.
Estimating the similarity of the target line parent plants with the virtual genomes from step one above using a marker association (Smith, Page 20, Paragraph 2014; Smith, Page 19, Paragraph 0203 – Smith, Page 20, Paragraph 0210).
Comparing the likelihood ratio from the marker association to a similarity threshold (Smith, Page 20, Paragraph 0210; Smith Figure 4).
Using the association analysis to predict traits in the target population and selecting parents (hypothetical parent genomes) which exceed the likeliness threshold (Smith, Page 20, Paragraphs 0214 and 0210).
Smith discloses that the log-likelihood function of transmitting the marker allele for the trait of interest into the target line (Smith, Page 19, Paragraphs 0201-0204), which can then be compared to the target line using the similarity threshold described in Figure 4 of Smith.
With relation to claim 3, Smith teaches the use of an identity-by-descent method. Specifically, Smith teaches likelihood ratio TDT tests which Smith describes as an association study and a type of identity by descent method (Smith, Page 4, Column 2, Paragraph 0045; Smith; Page 9, Column 2, Paragraph 0091; Smith, Page 19, Columns 1-2; Paragraph 0201-Paragraph 0204).
As it relates to claim 4 Smith teaches the use of haploid-based identity by descent methods including haplotype data in TDT-based association assays (Smith, Page 19,Paragraph 0203). Specifically, Smith teaches methods which take into account parent contributions individually (Smith, Page 9, Paragraph 0090).
As it relates to claim 7, Smith teaches that the target line is an inbred plant line (Smith, Page 10, Column 1, Paragraph 0097). Smith also teaches that target crop plants are canola plants (Smith, Page 3, Column 1, Paragraph 0018). Canola plants are a subset of rapeseed cultivars. Therefore, the canola plants of Smith are rapeseed plants.
As it relates to claim 22, Smith teaches crossing two parents to generate a traited progeny population having white cob color, where the progeny population has more members (entire population) having the trait of interest (white cob color) than the predicted number of offspring having the trait in the Likelihood ratio TDT Test (Smith, Page 20, Paragraphs 0214-0215).
As it relates to claim 24, Smith teaches using association analysis generated through the use of the Likelihood ratio TDT Test to predict the number of offspring from a cross which would inherit a trait of interest (white cob color) using association analysis through the use of the Likelihood ration TDT Test (Smith, Page 19, Paragraph 0204; Smith Page 20, Paragraph 0210).
This analysis uses haplotype genetic data from the parent population to identify the target genotype by identifying an association between a marker and a trait of interest (Smith, Page 19, Paragraph 0202; Smith, Page 19, Paragraph 0204; Smith Page 20, Paragraph 0210).
As it relates to claim 25, Smith teaches crossing two parents to generate a traited progeny population having white cob color, where the progeny population has more members (entire population) having the trait of interest (white cob color) than the predicted number of offspring having the trait in the Likelihood ratio TDT Test (Smith, Page 20, Paragraphs 0214-0215).
At the time of filing it would have been obvious to modify the method of Wardyn to incorporate the estimating a traited progeny population strategy of Smith. This would have been obvious because it would ensure that when producing the F1 hybrid progeny plants from which the doubled haploid plants are generated that the population of F1 progeny plants is large enough that it is likely that one of those plants will comprise very similar genetics to the target inbred line. This step ensures that the method is efficient and that it is likely that the homozygous inbred lines produced from the doubled haploid plants are very similar to the target inbred line. This would have been motivating because the benefit of this doubled haploid based method is that it allows for the generation of the traited target line without many additional steps and the providing a traited progeny line that is highly similar to the target line is critical. If the traited progeny line is sufficiently distinct from the target inbred line then another crossing step would be required which adds substantial time to that required to practice the method.
Further, it would have been obvious to modify the method of Wardyn in order to practice this method in Canola plants given that Smith teaches methods for improving the process of developing plant varieties in many crop plants including Canola, given the agronomic and economic benefits of improved methods for more rapidly producing elite Canola lines.
As such claims 2-4, 7, 21-22 and 24-25 are rejected as obvious under Wardyn in view of Smith.
Conclusion
Claims 1-9 and 19-26 remain rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached 7:30 to 5:00.
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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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/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663