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 .
Claim Status
Claims 1-22 and 24-25 remain pending.
Claims 10-18 remain withdrawn as being drawn to an unelected invention.
Claims 23 and 26 are newly cancelled.
Claims 1, 5, 19-20, 22 and 25 are newly amended.
Claims 1-9, 19-22 and 24-25 remain rejected.
Response to Applicant Arguments – Claim Objections
In response to applicant’s arguments and amendments to the claims the claim rejections of record against claims 1, 5, 19-20, 22 and 25 are withdrawn. Applicant’s cancellation of claims 23 and 26 renders the claim objections of record against those claims moot and they are withdrawn.
Response to Applicant Arguments – Indefiniteness
In response to applicant’s arguments and amendments to the claims the claim rejections of record against claims 1-9, 19-22 and 24-25 are withdrawn. Applicant’s cancellation of claims 23 and 26 renders the indefiniteness rejections of record against those claims moot and they are withdrawn.
Response to Applicant Arguments – Obviousness
Applicant’s arguments and amendments to the claims have been fully considered but are not found to be persuasive. While Applicant’s cancellation of claims 23 and 26 renders the rejections against those claims moot and they are withdrawn the remaining rejections of record are maintained. Applicant’s arguments are summarized and addressed below.
The amended independent claim is drawn to methods of generating a traited version of a target line comprising the following steps:
Providing an inbred target line descended from a cross of a first parent and a second parent.
Providing a version of at least one of the first parent and the second parent carrying a trait of interest where this parent was produced by crossing the parent with a donor parent comprising the trait, followed by backcrossing to recover the version.
Generating a traited version of a progeny population by crossing the first parent (or the version thereof) with the second parent (or the version thereof).
Selecting at least one traited version of the target line based on genetic similarity between the traited version of a target line and the target line, where the traited version of a target line is obtained without the need for multiple generations of inbreeding following the crossing of the parents.
Applicant urges that this is fundamentally different than the teachings of Wardyn and that the methods of Wardyn would not achieve the significant time savings of the instant method (Pages 11-13 of the Remarks dated 03/31/2026).
Applicant urges that Wardyn discloses that PH4CF1 was derived from a cross of two parents and that in contrast to Wardyn instant claims 1 and 19 require introgressing a trait into one of those parents, then re-crossing those parents to generate a new progeny population, and selecting from that population a traited version of the target line based on genetic similarity, while Wardyn teaches the opposite by adding traits directly to PH4CF1 through conventional backcross conversion. Wardyn, never suggests introducing a trait upstream and then re-crossing to regenerate PH4CF1 with the trait included.
Applicant urges that “The Action therefore combines the distinct roles of the “parent” and “target line” that the claims require to be separate entities in a defined pedigree relationship. Because this core method involving re-deriving the target line from its traited parents rather than directly backcrossing into the target line is entirely absent from Wardyn, the reference cannot anticipate or render obvious the claimed invention”.
This line of argument is not found to be persuasive because as set forth in the rejection of record the target line is not PH4CF1, rather it is a homozygous PH4CF1 progeny plant which is an inbred line produced by crossing PH4CF1 with another plant. As such the homozygous PH4CF1 progeny plant is one entity (The target inbred line) and PH4CF1 is another separate entity (The first or second parent plant).
In claim 1, Applicant describes the target line as follows: “an inbred target line descended from a cross of a first parent and a second parent”.
In lines 54-63 of column 34, Wardyn describes the PH4CF1 progeny plants as follows: “certain embodiments include a process for making a homozygous PH4CF1 progeny plant substantially similar to PH4CF1 by producing or obtaining a seed from the cross of PH4CF1 and another maize plant and applying double haploid methods to the F1 seed or F1 plant or to any successive filial generation”.
Wardyn clearly teaches a plant that they call a “homozygous PH4CF1 progeny plant” which is another name for “an inbred target line”. Further, Wardyn teaches explicitly that the homozygous PH4CF1 is produced by crossing PH4CF1 with another maize plant, the exact steps required by the claim.
As such Wardyn teaches both a target inbred line and a parent of that line. While Applicant urges that the office combines the “parent” and “target lines” there is no limitation in the claim that requires that the target inbred line and the parent line must be genetically or morphologically distinct, instead the target inbred line must be descended from a cross of a first parent and a second parent. While the homozygous PH4CF1 progeny plant is substantially similar to PH4CF1, it is made by crossing a plant of PH4CF1 with another plant and therefore the homozygous PH4CF1 progeny plants of Wardyn constitute a target inbred line according to the limitations required in the independent claim and therefore Applicant’s arguments are not found to be persuasive.
Applicant concludes the remarks drawn to the obviousness rejections of record by urging that Smith does not remedy the shortcomings of Wardyn. As noted above, Applicant’s proposed shortcomings of Wardyn do not appear to exist, therefore this argument is not found to be persuasive.
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.
This rejection is maintained for the reasons of record, because the amendments and remarks by Applicants in response to Office Action mailed on January 09, 2026, have been fully considered but not deemed persuasive. See above for the response to Applicant's remarks..
Claims 1, 5-6, 8-9 and 19-20 remain 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, without the need for multiple generations of inbreeding following said crossing the first parent or said version thereof with the second parent or said version thereof.
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 a traited version of the target homozygous PH4CF1 progeny plant, which 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 claims 5-6 and 8-9, 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 and 8-9 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 20, 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.
Claim 20 is rejected as obvious under Warden.
Claims 2-4, 7, 21-22 and 24-25 remain 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 remain rejected as obvious under Wardyn in view of Smith.
Conclusion
Claims 1-9, 19-22 and 24-25 remain rejected.
Finality
THIS ACTION IS MADE FINAL. 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.
Contact Information
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
Prosecution Insights