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 .
Prosecution Reopened
In view of the appeal brief filed on January 12, 2026, PROSECUTION IS HEREBY REOPENED. New grounds of rejection are set forth below.
To avoid abandonment of the application, appellant must exercise one of the following two options:
(1) file a reply under 37 CFR 1.111 (if this Office action is non-final) or a reply under 37 CFR 1.113 (if this Office action is final); or,
(2) initiate a new appeal by filing a notice of appeal under 37 CFR 41.31 followed by an appeal brief under 37 CFR 41.37. The previously paid notice of appeal fee and appeal brief fee can be applied to the new appeal. If, however, the appeal fees set forth in 37 CFR 41.20 have been increased since they were previously paid, then appellant must pay the difference between the increased fees and the amount previously paid.
A Supervisory Patent Examiner (SPE) has approved of reopening prosecution by signing below:
/Amjad Abraham/SPE, Art Unit 1663
Claim Status
Claims 1, 3-8, 13-18 and 21-24 remain pending.
Claims 13-18 and 21-24 remain withdrawn as being drawn to unelected inventions.
Claim 3 is newly amended.
Claims 1 and 3-8 are newly rejected.
Claim Objections
Claim 1 is objected to because of the following informalities: in the third and fourth lines the claim recites “providing an integrated quantitative framework across breeding and agronomy management,”. This appears to be missing a word after breeding and agronomy management or words before breeding. The claim is drawn to providing an integrated quantitative framework across breeding and agronomy management approaches and in order to improve claim syntax language to this affect should be added to the claim. Appropriate correction is requested.
Claim 2 is objected to because of the following informalities: the claim has been canceled but the text of the claim has not been deleted. Appropriate correction is required.
Claim 4 is objected to because of the following informalities: the claim recites “A method of synchronized breeding and agronomy for increasing yield, the comprises”. This appears to be missing several words after “increasing yield,”. The office suggests amending the claim to recite “increasing yield, the method comprising:”. Appropriate correction is required.
Claim 5 is objected to because of the following informalities: the claim recites “A method of integrating one or more agronomic practices (management) into early-stage breeding pipeline”. This appears to be missing a word between “into” and “early-stage”. The office suggests amending the claim to read “A method of integrating one or more agronomic practices (management) into an early-stage breeding pipeline”. Additionally, the claim recites “wherein the genotypic variations and the environmental conditions are optimized together based and not sequentially”. This recitation appears to have an extra word “based” which should be removed from the claim. Appropriate correction is required.
Response to Applicant Arguments – 35 USC § 112 (Indefiniteness)
In response to applicant’s amendments filed 09/10/2025, the indefiniteness rejection of record is withdrawn. New indefiniteness rejections are presented below.
Claim Rejections - 35 USC § 112
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 and 3-8, 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.
Claim 1 is drawn to a method of accelerating synchronized breeding and management practices. This claim includes the following steps:
providing an integrated quantitative framework across breeding (breeding component) and agronomy management (two agronomic management components) that form a gap analysis.
Predicting one or more improvements in crop productivity from the framework strategies.
Selecting a population of plants for breeding based on a predicted performance of one or more of the plants under a targeted management practice.
Combining a genetic component to synchronize breeding such that a breeding plant population is selected based on the gap analysis where the genetic component and the agronomy management components are optimized together and not sequentially.
Growing the selected plant population in a crop growing environment.
The claim is indefinite because it is not clear how step 4 summarized above, relates to the rest of the claim. Specifically, step 3 as summarized above, is drawn to a selecting step, then step 4 appears to be a second selecting step based on combining genetic and agronomy components to optimize them together such that a breeding plant population is selected based on that analysis.
It is not clear if this second selecting step further limits step 3 or if it is drawn to an additional step after step 3 or if it is an alternative step. As such the scope of the claim is not clear. Dependent claim 3 is included for depending on an indefinite claim and failing to limit the scope to definite subject matter.
In order to ensure compact prosecution the claim is being interpreted to comprise only the single selecting step described in 3 above and the limitations in the second selecting step described in step 4. above are not considered.
In claims 1 and 4-5 the recitations of “optimized together based on the gap analysis and not sequentially”, “optimized together and not sequentially” and “optimized together based and not sequentially” are indefinite. This is because the scope imparted on the claim by this limitation is not clear. Earlier in each of the claims, there are recitations of steps that must be carried out to perform the methods.
In claim 1 there is a required gap analysis which is described as “comprising a comparison of the experimental grain yield result with the predicted grain yield”. This indicates that the gap analysis involves comparing experimental data with a predicted dataset after which predictions on improvements in crop productivity are made and the plants are selected.
In claim 4 there are steps of providing a crop model, selecting a subset of management conditions based on the model, growing a population of plants, then applying selection criteria to the population of plants after which the genotype and agronomy management components are optimized together.
In claim 5, the genotypic variations and the environmental conditions are optimized together and not sequentially before crop growing environmental conditions and management practices are non-sequentially applied to a population of plants. After that application of conditions and management practices has taken place a subset of the population of plants are selected for further breeding advancement.
In applicant’s brief dated 01/12/2026, on page 13 applicant urges that because the reference teaches that the model was optimized based on the gap analysis and because plants were selected after the analysis that the two components were not optimized together rather than sequentially. This argument appears to be based on the idea that if the method has any steps at all then the different components are not optimized together and are instead optimized sequentially.
The language of applicant’s claims appears to contradict this position. For example, claim 1 recites the following steps: “comparison of the experimental grain yield result with the predicted result” which indicates that a prediction on grain yield is made using an integrated quantitate framework comprising a breeding component and at least two agronomic management components. Then, it appears that an experiment is conducted to measure experimental grain yield (Emphasis added). After that, a gap analysis is performed which can then be used to predict one or more improvement on crop productivity from the quantitative framework (Emphasis added). The next step is selecting a population of plants for breeding and then finally the selected plants are grown in a crop growing environment.
As such it is clear that applicant’s method requires steps in the same way that the reference discussed on page 13 of the brief requires steps. Given this in light of applicant’s arguments and the internal contradiction of the claim language, the meaning of “optimized together based on the gap analysis and not sequentially” is not clear.
To highlight areas of unclear scope, applicant urges that the reference does not teach synchronous optimization because the gap analysis identified an area for improvement which the model was then adjusted to reflect after which optimized plants were selected, however given the language of the claim, applicant’s method clearly follows sequential steps in the same way as taught in the reference.
Therefore, given the contradiction between the recitation of the phrases “optimized together” and “and not sequentially” and the step by step structure of the claimed method the meaning of “not sequentially” is not clear and as such the scope of the claims is indefinite and the claims are rejected. Claims 3 and 6-8 are rejected for depending on indefinite claims and failing to limit the scope of the claim to definite subject matter.
Claim 1 recites the limitations "the experimental grain yield" and “the predicted grain yield” in lines 6-7 of the claim. There is insufficient antecedent basis for this limitation in the claim.
Claim 3 recites the limitation "The method of claim 1, wherein the agronomic management is selected from the group”. There is insufficient antecedent basis for this limitation in the claim. This is because while claim 1 recites “agronomy management” and “at least two agronomic management components” it does not recite “agronomic management”. Further, in claim 1 “agronomy management” and “at least two agronomic management components” provide different scopes and therefore the scope of claim 3 will vary significantly based on which term the recitation of claim 3 further limits. Therefore, the scope of claim 3 is unclear and the claim is rejected as indefinite.
In claim 3 the recitation of “wherein the agronomic management is selected from the group” is indefinite. Claim 3 depends on claim 1 which recites “breeding and agronomy management” and also “agronomic management components”. It is not clear what “the agronomic management” of claim 3 is limiting and if it is limiting the integrated quantitative framework across breeding and agronomy management” it is not clear how this limitation would affect the agronomic management components that form a gap analysis
In claim 4 the recitation of “proving a crop model or other quantitative simulation to formulate one or more genotype by management approaches to breeding” is indefinite. The meaning of “proving” in this context is unclear. Is a prediction being proved to be correct or does prove have some other meaning in this context? The specification does not clarify the meaning of “proving”. Given that it is unclear what “proving a crop model of other quantitative simulation data” means the scope of the claim is not clear and claim 4 is rejected as indefinite.
In claim 4 the recitation of “selecting a subset of selected agronomic management conditions based on the crop growth model” is indefinite. This is because it is not clear what the “selected agronomic management conditions” are. Are these conditions that are produced using the crop growth model or other quantitative simulation data. Are they a list of components that are important to the breeder. Without knowing what these “selected agronomic management practices” are or how they are selected the scope of the claim is not clear. Are these selected conditions any group of conditions selected at all? Are these selected conditions “based on the crop growth model or the quantitative simulation data”?
As such the scope of step b. of claim 4 is unclear and therefore the claim is rejected as indefinite.
Claim 4 recites the limitations "the agronomic management conditions" in section d. of the claim. There is insufficient antecedent basis for this limitation in the claim. Step b. of the claim refers to “selecting a subset of selected agronomic management conditions”. It is unclear if the recitation of agronomic management conditions in section d. refers to the selected subset of selected agronomic management conditions, to the selected agronomic management conditions or to some other agronomic management conditions.
Claim 4 recites the limitations "selecting the plants" in section e. of the claim. There is insufficient antecedent basis for this limitation in the claim. Earlier in the claim, claim 4 recites “population of plants”, however given the language of section E. the “selecting the plants” step does not appear to refer to these populations of plants and therefore the scope of “selecting the plants” is not clear.
In claim 4 the recitation of “applying one or more selection criteria to the population of plants frown in the crop growing environments such that the selected plants are capable of expressing their genetic potential” is indefinite.
The scope of this limitation is not clear. Won’t plants express their genetic potential under any set of conditions? It is unclear what characteristics the selection criteria must possess in order for the selected plants to be capable of expressing their genetic potential. Given that the scope imparted on the claim by this recitation is unclear, the scope of claim 4 is unclear and the claim is rejected as indefinite.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 5 recites “agronomic practices (management)”, which includes the broad statement of “agronomic management” and the narrower statement “agronomic practices”. The claim is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Response to Applicant Arguments – 35 USC § 102
Applicants arguments and amendments filed 09/10/2025 have been fully considered, however applicant arguments are not found to be persuasive, see analysis below.
First, in response to applicant’s arguments the anticipation rejections of record have been reformatted in order to remove the evidentiary reference, Weller and to improve clarity by more directly mapping the limitations disclosed by Cooper onto the claims.
Second, the primary theme of applicant’s remarks appears to be that Cooper does not disclose methods to accelerate synchronized breeding and management practice including the feature of a gap analysis that includes a comparison of the experimental grain yield result with the predicted grain yield and importantly that Cooper does not disclose that the genetic and agronomic management components are optimized together.
Applicants arguments are not found to be persuasive because while the exact terminology used the claims differs in part from that found in Cooper, given the features of the method of Cooper, accelerated breeding and simultaneous optimization of the genetic component and the agronomy management component are inherent properties of the method of Cooper.
First, while the office action does not quote Cooper, on Page 1 of Cooper in the background section, Cooper provides motivation to accelerate breeding for complex traits. First Cooper describes the benefits of breeding cycles that use molecular breeding stating that “Breeding cycles can be accelerated because a genotype can be determined more quickly than a phenotype” making clear that accelerating breeding is beneficial and something to look for in a strategy (Cooper, Pare 1, Lines 5-6). Given this disclosure the ordinary artisan would understand that methods of using molecular breeding, such as the one disclosed by Cooper accelerate breeding practices.
Further, the method of Cooper does use a gap analysis because Cooper, compares predicted grain yield values to experimental grain yield, which allowed Cooper to identify discrepancies between the two, identifying variable soil depths in two fields as responsible for differences in yield (Cooper, Page 29, Lines 16-26).
Finally, the method of Cooper uses synchronized analysis of the genetic component and agronomic management components and accelerates breeding cycles. Specifically, in Example 7 of Cooper, Cooper discloses the application of the Crop Growth Model – Whole Genome Prediction (CGM-WGP) to optimize the breeding of a varied population of double haploids under variable management conditions (irrigation timing, irrigation amount and soil depth) (Cooper, Page 22, Lines 9-31). As such this data examines the yield of double haploids having varied genetics (Breeding component) under manipulation of irrigation quantity and irrigation timing at the same time. This clearly demonstrates that the breeding and agronomic management components are analyzed synchronously.
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 and 3-8 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cooper, WO 2016/069078 A1, Published May 6, 2016.
Claim 1 is drawn to methods of accelerating synchronized breeding and management practices comprising several steps which are outlined below.
Providing an integrated quantitative framework which forms a gap analysis between an experimental grain yield result with a predicted grain yield. Where the framework comprises:
a breeding component
at least two agronomic management components
Predicting at least one improvement in crop productivity from the framework.
Selecting a population of plants for breeding based on a predicted performance of one or more of the plants under a targeted agronomic practice.
Growing the selected plant population in a crop growing environment.
Of note, the claim includes an additional recitation after the selection step that appears drawn to a second selecting step. As noted above in the indefiniteness rejection, the scope of this recitation is not clear as at this point in the method a population of plants has already been selected for breeding based on a predicted performance of one or more of the population of plants under a targeted agronomic management practice so it is not clear what the second selecting step is referring to. Therefore, the claim is being interpreted to comprise only the single selecting step and the “Combining a genetic component with the agronomy management components to optimize these components together to synchronize breeding and gap analysis is used to select a breeding plant population” step is not examined.
With respect to claim 1, Cooper in example 7 on pages 22-31 discloses a method comprising the following steps:
Providing a framework (Crop growth model) to compare predicted grain yield versus the experimental grain yield (Cooper, Page 29, Lines 16-18) to identify areas that needed to be addressed in order to generate a more accurate model (A gap analysis between the predicted and experimental yields)(Cooper Page 29, Lines 18-26) which allowed for the selection of plants having certain yield parameters (Cooper, Page 31, Lines 3-11). This framework integrates the following components:
Breeding component: Cooper uses a MET dataset which comprises a collection of various distinct doubled haploid lines which differ in at least 86 single nucleotide polymorphic markers distributed across the 10 chromosomes (Cooper, Page 22, Lines 9-23).
Management Components:
Quantity of irrigation (Cooper, Page 22, Lines 24-27).
Timing of irrigation (Cooper, Page 22, Lines 24-27).
Cooper predicts an improvement in crop productivity from this framework, specifically, that increased soil depth leads to greater yield (Cooper, Page 29, Lines 16-30). Cooper notes that in the SFS environment the experimental yields were lower than the predicted yields and predicts that this is because the soil depth in this environment is lower than that of the FS environment, thus predicting that greater or lesser soil depth is associated with greater or lower yields (Cooper, Page 29, Lines 16-30).
Cooper then discloses ranking individual double haploid plants and selecting sets of double haploid plants for highest yield under the water stress conditions, based on the analysis by the crop growth model(Cooper, Page 31, Lines 3-11).
In parts e-g of claim 1 on page 35, Cooper clarifies that after selecting sets of haploid plants (breeding pairs), these pairs having desired traits (high yield under water stress conditions) would be grown, crossed and their offspring would be grown (cooper, Page 35, Claim 1).
Mapping the disclosure of Cooper over the limitations of the instant claim, make clear that in the embodiment of Example 7, Cooper discloses all of the limitations of instant claim 1 and therefore claim 1 is rejected as anticipated by Cooper.
With respect to claim 3, Cooper discloses all of the limitations of claim 1, see above. Further, Cooper discloses water management strategies to induce water stress in the double haploid maize plants (Cooper, Example 7, Page 22, Line 24 – Page 23, Line 7).
Independent claim 4 is drawn to a method of synchronized breeding and agronomy for increasing yield through the following steps:
providing a crop model to formulate a genotype by management approach to breeding.
Selecting agronomic management conditions applicable to a population of plants at an early stage in a breeding pipeline based on the crop growth model.
Growing the target plant population under the agronomic management conditions.
Applying a selection criteria to the plants growing under the agronomic management conditions.
Selecting plants best suited for a target environment or management practice for further breeding advancement.
With respect to claim 4, in Example 7 on Pages 22-31, Cooper discloses a method of increasing yield in selected plants by analyzing the impact of plant genetics (breeding) and water management strategy (agronomy) which uses the following steps(Cooper, Page 22, Lines 1-8; Cooper Page 22, Lines 24-27; Cooper, Page 30, Lines 15-27; Cooper, Page 31, Lines 1-23):
Using a crop growth model to formulate an approach to plant breeding that uses predictions based on integrating genotypic information and management practice in order to predict combinations of plants to breed (Cooper, Page 23, Lines 23-31; Cooper, Page 22, Lines 9-23; Cooper Page 22, Lines 24-27; Cooper, Page 30, Whole Page).
Using the crop growth model to select agronomic management conditions, like soil depth and timing and quantity of irrigation (Cooper, Page 29, Lines 16-30; Cooper, Page 22, Lines 9-14).
The double haploid plants were grown under the low soil depth and water stress conditions (Cooper, Page 28, Lines 16-20; Cooper, Page 29, Lines 16-26).
Plants were then ranking and selection criteria were applied based on the crop growth model (Cooper, Page 31, Lines 3-11).
These selection criteria (varied selection intensities) were then used to select sets of double haploid plants (Cooper, Page 31, Lines 3-11). Later in the disclosure Cooper makes clear that plants selected using the model are used in breeding methods by crossing the sets of double haploids and growing these offspring (Cooper, Page 35, Claim 1, Steps e.-g.).
With respect to claim 5, Cooper discloses a method of integrating one or more agronomic practices (management) into early-stage breeding pipeline through the use of a CGM (Cooper, Example 7, Page 22, Lines 2-8) to examine the effect of irrigation and drought stress (Cooper, Example 7, Page 22, Lines 24-31) on the yield of a heterozygous population of double haploid maize hybrid plants (Cooper, Example 7, Page 22, Lines 9-23).
Cooper, discloses that the method comprises simultaneously applying irrigation techniques and drought stress (Cooper, Example 7, Page 22, Lines 25-27) to a population of plants comprising genotypic variations (Cooper, Example 7, Page 22, Lines 17-23).
The crop growing conditions (drought stress) are informed by a crop growth model (Cooper, Example 7, Page 23, Lines 24-25) which was modified to simulate soil water balance, transpiration and growth response to water deficit (Cooper, Example 7, Page 24, Lines 1-4). Cooper is drawn to methods of selecting breeding populations and Cooper discloses that these methods include a final step of selecting the best performing plants for a breeding program (Cooper, Page 35, Claim 1, Preamble and Steps E-G).
With respect to claim 6, Cooper discloses all of the limitations of claim 5, see above. Further, Cooper discloses that the agronomic practice was irrigation (Cooper, Example 7, Page 22, Lines 24-31).
With respect to claim 7, Cooper discloses all of the limitations of claim 5, see above. Further, Cooper discloses the environmental stress was water stress (drought stress)(Cooper, Example 7, Page 24, Lines 1-4).
With respect to claim 8, Cooper discloses all of the limitations of claim 5, wherein the method uses a crop growth model (Cooper, Example 7, Page 23, Lines 23-31).
Response to Applicant Arguments – Double Patenting
In response to the terminal disclaimer filed 09/10/2025 over US Patent No. 11,985,930 B2, the double patenting rejections of record are withdrawn.
Conclusion
All claims are rejected.
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.
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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
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