DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Herein, “the previous Office action” refers to the Non-Final Rejection filed on 12/29/2025.
Amendments Received
Amendments to the claims were received on 3/30/2026.
Priority
As detailed on the Filing Receipt filed 4/13/2022, the instant application claims priority to as early as 2/5/2021. At this point in prosecution, the claims are being accorded the earliest claimed priority date.
Claim Status
Claims 9, 13 and 19 are canceled.
Claims 1-8, 10-12, 14-18 and 20 are pending, and under examination.
Withdrawn Objections/Rejections
The objection to claim 11 is hereby withdrawn in view of Applicant’s amendment of the claim to correct a minor grammatical informality.
The rejection of claims 11-18 and 20 under 35 USC § 112(b), as being indefinite, is hereby withdrawn in view of Applicant’s amendment of claims 11 and 18 (as noted at pg. 5, para. 3 of the Remarks filed 3/20/2026) to render claim language concerning use of the system as definite, and cancelation of claim 13. See ‘Claim Interpretation’ section for further details regarding amended claim language.
The rejection of claim 13 under 35 USC § 101, as being directed to nonstatutory subject matter, is hereby withdrawn in view of Applicant’s cancelation of the claim.
The rejection of claim 13 under 35 USC § 103, as being unpatentable over Jefferies, in view of Soleimani, is hereby withdrawn in view of Applicant’s cancelation of the claim.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art (MPEP 2111-2111.01). This section documents the examiner’s interpretation of certain recited claim language.
Claim 11 recites the system component of a “breeding pipeline” (lines 3 and 17), and further specifies that the breeding pipeline is “of a target environmental region” (line 3).
The specification states that “As used herein, the term ‘breeding pipeline’ refers to a population of germplasm or plants to be used in a breeding program to generate new cultivars” (pg. 7, para. 4 – pg. 8, para. 1), i.e., a physical population of germplasm or plants for which the recited use is indicated. The courts have held that where an explicit definition is provided by the applicant for a term, that definition will control interpretation of the term as it is used in the claim (Toro Co. v. White Consolidated Industries Inc., 199 F.3d 1295, 1301 (Fed. Cir. 1999)). For purposes of prosecution, the recited component is interpreted accordingly.
Claims 11 and 18 recite the following claim language:
“is to be introgressed” (lines 6 and 13);
“for use in introgressing… through 2 or fewer backcrosses” (claim 18, lines 1-3);
The above phrases are interpreted as indicating intended uses of the claimed system, and various system components, rather than requiring such uses (i.e., as method limitations).
Response to Arguments - Claim Rejections Under 35 USC § 101
In the remarks filed 3/30/2026, Applicant traverses the rejection under 35 USC § 101 and presents supporting rationale.
Applicant cites description in para. 0017 of the specification for support, and alleges that claim 11 is integrated into a practical application that provides technical improvements to classic trait introgression methods by providing a computing device in communication with a data structure and configured to perform functions of an improved trait introgression process (pg. 6, para. 2 – pg. 7, para. 1).
As noted by Applicant therein, the cited specification passage states that identification and use of an intermediate recurrent parent in trait introgression processes significantly reduces time required to develop new cultivars, reduces operational cost, and achieves the same level of probability of success as classic trait introgression methods.
Claims 11 and dependents thereof are directed to a system comprising plants, and a computing device, with recited functional capabilities and intended uses. The described advantages regard the relative efficiency and economical nature of a trait introgression process that the claimed system is capable of implementing, relative to existing trait introgression processes. The described advantages do not regard improvements to functioning of the computer device, or other technical components of the system, relative to technology previously employed in the field of the invention.
Relative improvement of a method, albeit implemented by a computer, is not inherently equivalent to an improvement of the computer. For example, the court of Trading Technologies Int’l v. IBG, 921 F.3d 1084, 1093-94 (Fed. Cir. 2019), held that a claimed user interface did not confer eligibility, although provided relative improvement to an implemented business process of market trading, because it did not improve the implementing computer itself simply by virtue of implementing said process thereon.
Description of the advantageous nature of an introgression technique that the system is capable of implementing is found unpersuasive regarding subject matter eligibility of the claimed system itself, therefore the rejection is maintained.
Claim Rejections - 35 USC § 101
35 USC § 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 11-12 and 14-18 and 20 are rejected under 35 USC § 101 because the claimed invention is directed to non-statutory subject matter. "Claims directed to nothing more than abstract ideas, natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). This rejection is maintained from the previous Office action, and has been revised to address the amended claims (filed 3/30/2026).
Abstract ideas include mathematical concepts (e.g., formulas, equations and calculations), and mental processes (concepts which may be performed in the human mind, e.g., evaluating, analyzing or organizing information) (MPEP 2106.04(a)).
Natural phenomena include principles, relations, and products that are naturally occurring or do not have markedly different characteristics compared to what occurs in nature (MPEP 2106.04(b)).
The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than judicial exceptions.
Step 1: The Four Categories of Statutory Subject Matter (MPEP 2106.03)
The claims are directed to a system, which falls under at least the ‘composition of matter’ category of statutory subject matter.
Step 2A, Prong One: Whether the Claims Set Forth or Describe a Judicial Exception (MPEP 2106.04 § II.A.1)
‘Mathematical concepts’ include relationships between variables and numbers, numerical formulas or equations, or acts of calculation, which need not be expressed in mathematical symbols (MPEP 2106.04(a)(2) § I). The claims recite the following element which encompasses a mathematical concept, at least under the broadest reasonable interpretation consistent with the specification:
“based on a predetermined distance threshold”, i.e., (claim 11), i.e., according to calculated metrics; and
“selecting at least one intermediate recurrent parent… [which] is centric in genetic distance relative to other members of the at least one recipient parent group” (claim 11), e.g., performing k-medoids clustering based on a pairwise distance metric.
The above elements encompass and delimit acts of calculation, which constitute mathematical concepts.
‘Mental processes’ include processes that can be performed in the human mind at least with use of a physical aid, e.g., a slide rule or pen and paper (MPEP 2106.04(a)(2) § III). The recited acts of calculation are practicably performable in the human mind, and therefore additionally encompass mental processes. The claims further recite the following elements, which encompasses acts that are practically performable in the human mind:
“group[ing] the population of recipient parents… into at least one recipient parent group” (claim 11), i.e., organizing data, wherein:
“the at least one recipient parent group… further comprises up to ten other members of the population of recipient parents” (claim 16), i.e., up to 11 set members are grouped,
“at least one member of the at least one recipient parent group is a member of a second recipient parent group” (claim 17), i.e., grouped set members are also members of other groups.
The human mind is capable of selecting a subset of set members, hence, the encompassed act constitutes a mental process.
Mathematical concepts and mental processes constitute enumerated groups of s (MPEP 2106.04(a)(2) §§ I and III). Hence, the claims recite elements that constitute an abstract idea.
‘Products of nature’ include naturally occurring products, and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart (MPEP 2106.04(b) § II). The claims recite the following elements that encompass products of nature, at least under the broadest reasonable interpretation consistent with the specification:
“a breeding pipeline of a target environmental region” (claim 11), e.g., a population of germplasm or plants that naturally occur in a particular environmental region (see ‘Claim Interpretation’ section);
“a donor parent plant comprising the at least one agronomic trait of interest” (claim 11), e.g., a naturally occurring plant, wherein:
“the a least one agronomic trait of interest is associated with any combination of herbicide tolerance, insect control… or tolerance to nitrogen stress” (claim 20), i.e., the donor plant exhibits a particular phenotype; and
“a population of recipient parents” (claim 11), e.g., a population of naturally occurring plants, wherein:
“the first recipient parent group is one of a plurality of recipient parent groups… [and] each member of the population of recipient parents is associated with at least one of the plurality of recipient parent groups, and… the first intermediate recurrent parent is one of a plurality of intermediate recurrent parents… each of [which] is associated with at least one of the plurality of recipient parent groups” (claim 12), e.g., the ‘recipient parent’ plants are associated with a plurality of populations of naturally occurring plants,
“a genetic distance between any two members of the at least one recipient parent group is at most 65% according to identity by descent” (claim 14), i.e., the plants exhibit a particular naturally occurring level of genetic similarity, and
“a genetic distance between any two members of the at least one recipient parent group is at most 80% according to identity by descent” (claim 15), i.e., the plants exhibit a particular naturally occurring level of genetic similarity.
The claims thus recite elements that constitute a natural phenomenon.
Hence, the claims recite numerous elements that, individually and in combination, constitute an abstract idea and natural phenomenon. The claims must therefore be examined further to determine whether they integrate these judicial exceptions into a practical application (MPEP 2106.04(d)).
Step 2A, Prong Two: Whether the Claims Contain Additional Elements that Integrate the Judicial Exception(s) into a Practical Application (MPEP 2106.04 § II.A.2)
The claims recite the additional element of “a computing device in communication with a data structure and configured to” (claim 11) perform claimed functions.
The claims do not describe any specific computational steps by which the computing device performs or carries out the judicial exceptions, nor do they provide any details of how specific structures of the computing device are used to implement these functions. The claims state nothing more than that a computing device is configured to perform functions that constitute judicial exceptions, and are therefore considered mere instructions to apply the judicial exceptions using a generic computer. As such, the claims do not integrate that abstract idea into a practical application (MPEP 2106.04(d) § I and 2106.05(f)).
The claims further recite the following elements:
“a plant derived from at least one traited member of the population of recipient parents is for use in the breeding pipeline” (claim 11); and
“the donor parent plant comprising the at least one trait of interest is for use in introgressing said trait of interest to the intermediate recurrent parent through 2 or fewer backcrosses” (claim 18).
These elements indicate intended uses, thus merely linking the claimed system to particular fields of use (see ‘Claim Interpretation’ section), and do not meaningfully limit the execution of system functions. Field of use limitations are insufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(h)).
No further additional elements are recited.
When the claims are considered as a whole: they do not improve the functioning of a computer, other technology, or technical field (MPEP 2106.04(d)(1) and 2106.05(a)); they do not apply the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition (MPEP 2106.04(d)(2)); they do not implement the judicial exceptions with, or in conjunction with, a particular machine (MPEP 2106.05(b)); they do not meaningfully limit the judicial exceptions by effecting a transformation or reduction of a particular article to a different state or thing (MPEP 2106.05(c)); and they do not apply or use the judicial exceptions in some other meaningful way beyond linking the use of the judicial exceptions to a particular field of commercial use and/or technological environment (i.e., selective plant breeding; MPEP 2106.05(h)).
Therefore, the claims do not integrate the judicial exceptions into a practical application. See MPEP 2106.04(d) § I.
Because the claims recite judicial exceptions, and do not integrate the judicial exceptions into a practical application, the claims are directed to the judicial exceptions. Claims that are directed to judicial exceptions must be examined further to determine whether recited additional elements that are not the judicial exceptions render the claims significantly more than the judicial exceptions. Additional elements besides the judicial exceptions may constitute inventive concepts that are sufficient to render the claims as providing significantly more (MPEP 2106.05).
Step 2B: Whether the Claims Contain Additional Elements that Amount to an Inventive Concept (MPEP 2106.05)
As noted above, several recited additional elements amount to insignificant extra-solution activity. Mere addition of insignificant extra-solution activity does not amount to an inventive concept that would render the claims significantly more than the recited abstract idea, particularly when the activities are well-understood or conventional (MPEP 2106.05(g)). The conventionality of recited additional elements that amount to insignificant extra-solution activity must be further considered.
Recited additional elements amounting to insignificant extra-solution activity encompass the following structures and processes, which are indicated as known commercial activity within the field of the invention by the instant specification (see MPEP 2106.07(a) § III):
Introgression of an agronomic trait of interest through backcrossing (pg. 1, para. 0003: “Breeders are continually developing new cultivars through various plant genetic improvement programs… [that] traditionally rely on introgression of alleles or genetic constructs conferring new or favorable traits from the genome of one line into the genome of an elite line though classic trait introgression methods”; pg. 5, para. 0016: “The combination of desirable traits with an elite genome to generate new cultivars traditionally occurs through classic trait introgression methods… where a favorable or new trait from a donor plant is introgressed into a recipient plant through repeated backcrosses of the donor parent carrying the desired trait”).
Hence, the encompassed activity is considered well-understood, routine and conventional. Well-understood, routine and conventional activities are insufficient to constitute an inventive concept that would render the claims significantly more than judicial exceptions (MPEP 2106.05(d)).
Mere indications of field of use are similarly insufficient to constitute an inventive concept that would render the claims significantly more than judicial exceptions (MPEP 2106.05(h)).
When the claims are considered as a whole, they do not integrate the judicial exceptions into a practical application; they do not confine the use of the judicial exceptions to a particular technology; they do not solve a problem rooted in or arising from the use of a
particular technology; they do not improve a technology by allowing the technology to
perform a function that it previously was not capable of performing; and they do not
provide any limitations beyond generally linking the use of the judicial exceptions to a particular field of commercial use and/or technological environment (i.e., selective plant breeding; MPEP 2106.05(h)).
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole, are directed to judicial exceptions and lack an inventive concept. Hence, the claimed invention does not constitute significantly more than the judicial exceptions, so the claims are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Response to Arguments - Claim Rejections Under 35 USC § 103
In the remarks filed 3/30/2026, Applicant traverses the rejections under 35 USC § 103 and alleges that the cited documents do not teach or suggest all features of any claim (pg. 7, para. 2).
Applicant alleges that cited portions of Jefferies have been taken out of context to support an assertion of obviousness, and do not teach or suggest grouping recipient parents by genetic distance, but rather concern comparison of a single recurrent parent to various other lines as evidenced by further portions of Jefferies (pg. 7, para. 3 – pg. 8, para. 1).
On pg. 12 (para. 2), Jefferies discusses the application of genetic distance estimates between parents to choose donor and recurrent parents, and mentions a theory that more similar parents would necessitate fewer backcrosses. Jefferies also notes therein that there is little evidence in the literature of attempts to assess the potential of this application. Further portions of the thesis present a novel attempt to assess this use of genetic distance estimates.
On pgs. 155-156 (spanning para.), Jefferies discloses cluster analysis of all cultivars and breeder lines, via the Unweighted Pair Group Method with Arithmetic mean (UPGMA, a hierarchical clustering method), based on their pairwise genetic distances. The fact that Jefferies does not ipsis verbis teach clustering of recipient parents as claimed is not viewed as a fatal deficiency of the reference. The term “recipient parents” simply defines a functional role served by particular cultivars in a breeding scheme. Thus, the argument is found unpersuasive.
Applicant alleges that Soleimani, while teaching implementation of k-medoids clustering to generate a representative core collection from a large population of genotypes, does not teach or suggest utilizing a clustering method as a step for introducing a trait of interest into a desired population of plants, let alone for grouping, by genetic distance, the population of recipient parents as claimed (pg. 9, para. 1).
Soleimani unambiguously describes the application of their clustering methods (e.g., k-medoids) to grouping and selecting germplasm, having traits of interest, for plant breeding purposes (pg. 2, l. column; pg. 6, r. column). Indeed, the described clustering techniques are presented in terms of their utility for plant breeding from the outset - the first sentence of the article reads as follows: “Germplasm collections are an important source of natural genetic diversity and provide a source of novel traits for sustainable crop improvement” (pg. 2, l. column).
The fact that Soleimani specifically teaches application of k-medoids clustering to grouping germplasm, rather than grouping of recipient parents (as claimed), is not viewed as a fatal deficiency of the reference. Jefferies, applied in combination with Soleimani, explicitly describes introgression of traits into “germplasm” (pg. 4, para. 1). In this way, Jefferies indicates that “germplasm” can serve in the functional role “recipient parents”. Indeed, the instant specification corroborates this understanding by defining the claimed breeding pipeline as “a population of germplasm or plants” (para. 0065). Thus, the argument is found unpersuasive.
Applicant alleges that the rejection has improperly utilized the application as a ‘roadmap’ to piece together teachings from portions of the cited art (i.e., improper hindsight analysis), since the art has not been shown to give any specific direction leading to the claimed invention from amongst numerous possible parameters (pg. 9, para. 2 – pg. 10, para. 2).
Jefferies discloses the process of trait introgression from donor parents to recurrent parents, suggests a functional advantage to selection of donor and recurrent parents according to minimal genetic distance, and discloses clustering of all cultivars (i.e., parents) according to genetic distance.
As the courts have held, a person of ordinary skill in the art “must be presumed to know something about the art apart from what the references disclose” (In re Jacoby, 309 F.2d 513,516 (CCPA 1962)). As one of ordinary skill in the art would be aware, each of the terms “donor parent”, “intermediate recurrent parent”, “recurrent parent” and “recipient parent” define the functional role of a given plant lineage in a given plant breeding scheme – that is, a particular plant lineage could serve as a donor parent in one breeding cycle and a recipient parent in another.
As the courts have held, “A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton” (KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421 (2007)). Selecting a ‘recipient parent’ from a first introgression cycle as the ‘donor parent’ of a second introgression cycle, and keeping the pool of recipient parents otherwise the same, would arrive at the claimed invention – the selected parent former recipient, now donor) playing the claimed role of an ‘intermediate recurrent parent’. Repetition of the disclosed process of introgression, and selecting parents in this manner, is considered to be within the technical skills and creative abilities of a person of ordinary skill in the art.
Jefferies suggests minimization of pairwise genetic distance between parents, however, the genetic distance-based cultivar clustering method disclosed therein does not produce clusters having a centric (minimal-distance) member as claimed. Soleimani discloses clustering germplasm according to genetic distance via k-medoids, producing clusters each with one centric member having minimal genetic distance to all other cluster members, to provide core collections that preserve novel trait diversity and, among other applications, can be utilized for plant breeding.
The failure of these references to teach, ipsis verbis, particular limitations at issue does not preclude their relevant teachings rendering these limitations as obvious. The rejection under § 103 includes rationale explaining obviousness of the claimed invention, in light of relevant teachings of the prior art, and does not rely on Applicant’s disclosure. Thus, the argument is found unpersuasive.
For the above reasons, the arguments are unpersuasive and the rejection is maintained.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 USC §§ 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 USC § 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.
The factual inquiries for establishing a background for determining obviousness under 35 USC § 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 USC § 102(b)(2)(C) for any potential 35 USC § 102(a)(2) prior art against the later invention.
Claims 1-8, 10-12, 14-18 and 20 are rejected under 35 USC § 103 as being unpatentable over Jefferies (‘Marker assisted backcrossing for gene introgression in barley (Hordeum vulgare L.)’ [thesis], University of Adelaide; published September 2000; previously cited), in view of Soleimani et al (Frontiers in Plant Science 11: article 1040, pp. 1-11; published 7/8/2020; previously cited). This rejection is maintained from the previous Office action, and has been revised to address the amended claims (filed 3/30/2026).
Claim 1 recites a method of deploying at least one agronomic trait of interest into a population of recipient parents, comprising:
a) grouping, by genetic distance, the population of recipient parents into at least a first recipient group, wherein the population of recipient parents lacks said at least one agronomic trait of interest;
b) selecting at least one intermediate recurrent parent from the at least first recipient parent group, wherein:
1. the at least one intermediate recurrent parent is centric in genetic distance relative to other members of the group;
c) introgressing the at least one agronomic trait of interest from a donor parent to a first intermediate recurrent parent, wherein:
1. said introgressing comprises 2 or fewer backcrosses; and
d) introgressing, through backcrossing, the at least one agronomic trait of interest from the first recurrent parent to other members of the first recipient group.
With respect to claim 1, Jefferies discusses “conventional and marker assisted backcrossing, and the application of backcrossing in plant breeding (see pg. VII, Table of Contents), specifically to the development of wheat and barley cultivars (pg. 1, para. 2; pg. 2, para. 3), and discloses:
a) “Genetic distance analysis” wherein “[a] genetic distance matrix was used for cluster analysis using the Unweighted Pair Group Method of Averages (UPGMA)” (pg. 155, para. 4 – pg. 156, para. 1), and “using genetic distance estimates between parents as a tool for choosing donor and recurrent parents… the more similar the donor and recurrent parents, the fewer backcrosses required” (pg. 12, para. 2), i.e., grouping, by genetic distance, a population of recipient parents;
b) “choice of a suitable recurrent parent” from among “recurrent parent candidates” (pg. 10, para. 3); and
c) “The backcross method involves crossing between a… parent contributing the gene or genes that control [a] desired trait… commonly designated the donor parent… [and a] parent into which genes are to be introgressed… termed the recurrent parent… The conventional backcross method… begins with hybridisation between the donor and recurrent parent followed by successive crosses between selected progeny carrying the desired new trait and the recurrent parent” (pg. 4, paras. 2-3), wherein:
1. “many wheat breeders did not use the full backcross method to reconstitute the recurrent parent, but used only one, two or three backcrosses to retain the benefits of transgressive segregation for agronomic characters such as grain yield” (pg. 14, para. 4).
Jefferies discusses application to “introgression of agronomically important traits” (pg. 2, para. 4), wherein the recipient parents initially lack the agronomic trait of interest. Jefferies also discusses the introgression of valuable genetic loci into elite breeding lines, which “can [subsequently] be either, released commercially or used as parents” (pg. 33, para. 4). In this way, Jefferies discloses further introgressing a trait from a recurrent parent (i.e., a line to which the trait has previously been introgressed).
Jefferies does not explicitly disclose introgressing an agronomic trait from a recurrent parent to other members of a recipient parent group. However, this is merely an embodiment of the disclosed introgression process wherein a lineage which served as a ‘recurrent parent’ in a first iteration is used as the ‘donor parent’ and crossed with a different recipient parent lineage for a second iteration. In this way, the disclosure of Jefferies is considered to make obvious introgressing the trait from a first intermediate recurrent parent to other members of a recipient parent group.
Jefferies does not disclose selecting at least one recurrent parent that is centric in genetic distance relative to other candidates.
Soleimani discusses management and utilization of germplasm collections as sources of traits for crop improvement, teaching that “Breeders seek to improve yield performance by exploiting favorable traits associated with tolerance against biotic and abiotic stress. Germplasm collections from major crops have increased in size and number worldwide… lead[ing] to problems and complications in the characterization, evaluation, utilization and maintenance of germplasm… to select core sets of these collections… [d]ifferent methods are available… with respect to phenotypic and genotypic data. These methods could be used to select genetically diverse genotypes for carrying out different scientific research before a large number of genotypes are phenotyped, thus excluding genotypes that would show the same behavior… by eliminating the need for an additional phenotyping step, these approaches could accelerate… breeding programs” (pg. 6, r. column, citations omitted).
Soleimani further discusses application of “general clustering approaches… available to subdivide a large data set into small groups with maximum genetic diversity between groups” (pg. 1, Abstract), and presents an experimental study wherein “genotypes were clustered into… groups by using the k-medoids clustering method” (pg. 4, l. column) wherein “K-medoids… minimiz[es] the distance between data points within a cluster to the respective cluster center… in k-medoids the cluster center needs to be a real object of the collection” (pg. 3, l. column).
Soleimani presents method quality assessment wherein “genetic metrics were applied to assess the quality of different core set selection methods… For such an objective the average A-NE”, accession-to-nearest-entry, “value should be as small as possible. An average A-NE value equal to zero indicates a minimal distance between genotypes… the k-medoids… core sets did the best job… with the lowest average value of A-NE observed” (pg. 7, l. column; see pg. 2, r. column for definition of ‘A-NE’ as a genetic distance metric). In other words, the applied clustering method effectively groups a population, by genetic distance, such that each group comprises a member centric in genetic distance relative to other members of the group.
In this way, Soleimani teaches that selecting plant lineages centric in genetic distance relative to other members of a considered group of lineages would allow users to avoid redundant breeding with parents that would exhibit the same phenotypic behavior.
With respect to claim 2, Jefferies teaches that “For some traits, it is possible to select from a range of donor parents” (pg. 2, para. 2), and exemplifies a breeding process wherein “backcross populations used… were developed from two recurrent parents” (pg. 71, para. 5). Jefferies further discusses “a backcross breeding program to introgress stem rust resistance into 10 adapted Australian wheat cultivars”, wherein “[w]idely adapted cultivars including Insignia, Bencubbin and Dirk were chosen as recurrent parents” (pg. 7, para. 1). Jefferies thereby exemplifies selection of a plurality of recurrent parents.
Furthermore, the selection of a core collection of accessions having minimal within-cluster genetic distance, according to the k-medoids method taught by Soleimani (pg. 4, l. column), is considered equivalent to selection of a plurality of recurrent parents associated with a plurality of recipient groups as claimed.
With respect to claim 3, Jefferies discloses that “The conventional backcross method… begins with hybridisation between the donor and recurrent parent followed by successive crosses between selected progeny carrying the desired new trait and the recurrent parent” (pg. 4, para. 3). The claimed introgression from a recurrent parent to other recipient parents is merely an embodiment of the disclosed multi-introgression process.
With respect to claims 4-5, Jefferies exemplifies a breeding process wherein “The measure of distance among cultivars was the covariance of allele frequencies summed for all fragments scored. The genetic distance matrix was used for cluster analysis using the Unweighted Pair Group Method of Averages (UPGMA)” (pg. 155, para. 4 – pg. 156, para. 1), wherein “The most genetically different parents were the Algerian landrace Sahara and the Japanese malting quality cultivar, Amagi Nijo (GD = 0.139)” (pg. 156, para. 3), i.e., genetic distance of 13.9%. In other words, a genetic distance between any two members is ≤ 65%, and is ≤ 80%, according to identity by descent.
With respect to claim 6, Jefferies exemplifies a breeding process wherein “Four donor parents were chosen for the development of BC1 populations… BC1 F2 populations were created from crosses between the four donor parents and the recurrent parent” (pg. 152, paras. 2-3). Jefferies thereby exemplifies utilizing a group of parents comprising one recurrent parent and further comprising zero (≤10) other recipient parents. See In re Mochel, 470 F.2d 638, 176 USPQ 194 (CCPA 1974).
With respect to claim 7, Jefferies discloses techniques for “simultaneous selection for multiple traits” (pg. 21, para. 1), comprising “introgressing several traits in the single program… with the use of several backcross streams, introgressing each trait in a separate backcross stream and then merging the streams near or at the final cross… the major advantage would be in the selection [of] desirable recombinants for several traits almost simultaneously within the final merged population… if more than one marker linked trait is carried by a single donor parent… the traits can be selected simultaneously” (pg. 23, para. 4). Jefferies thus teaches a method utilizing multiple backcross streams, wherein given members of a single population are parents in multiple recipient groups.
With respect to claim 8, Jefferies discloses the application of the backcrossing method in plant breeding (see pg. VII, Table of Contents), i.e., wherein the population of recipient parents consists of plants.
With respect to claim 10, Jefferies exemplifies “agronomic traits to be considered… includ[ing] resistance to cereal cyst nematode (CCN) (Heterodera avenae), resistance to barley leaf scald (Rhyncosporium secali), [and] resistance to barley yellow dwarf virus (BYDV)” (pg. 2, para. 5), i.e., resistance to plant pathogens.
Claim 11 recites a system for use in deploying at least one agronomic trait of interest into a population of recipient parents for use in plant breeding, comprising:
a) a breeding pipeline of a target environmental region;
b) a computing device in communication with a data structure and configured to:
1. group the population of recipient parents, into which at least one agronomic trait is to be introgressed, into at least one recipient parent group based on a predetermined genetic threshold, and
2. select at least one intermediate recurrent parent from the recipient parent group, wherein each recipient group comprises at least one recurrent parent centric in genetic distance relative to other members;
c) a donor parent plant comprising the at least one agronomic trait of interest; and
d) a population of recipient parents into which at least one agronomic trait is to be introgressed;
e) wherein a plant derived from at least one traited member of the population of recipient parents is for use in the breeding pipeline.
With respect to claim 11, Jefferies discusses “conventional and marker assisted backcrossing, and the application of backcrossing in plant breeding (see pg. VII, Table of Contents), and describes applications wherein:
a) plant cultivars are separated into “major geographic/selection environment groups” (pg. 164, para. 1), i.e., breeding pipelines of target environmental regions;
b) “Genetic distance analysis… was carried out using… a Macintosh computer software package” (pg. 155, para. 4), i.e., a computing device in communication with a data structure and configured to perform functions, wherein:
1. “[a] genetic distance matrix was used for cluster analysis using the Unweighted Pair Group Method of Averages (UPGMA)” (pg. 155, para. 4 – pg. 156, para. 1) whereby “cluster analysis of AFLP”, amplified fragment-length polymorphism, “data from the 21 selected cultivars and breeding lines… separated Australian breeding germplasm into distinct clusters with strong pedigree links” (pg. 164, para. 2), i.e., grouping recipient parents by genetic distance, via a computing device, and
2. “The elite Australian malting quality cultivar Sloop was chosen as the single recurrent parent… [it] is widely adapted to the southern Australian barley growing areas and is deficient in several important agronomic traits… (e.g. cereal cyst nematode resistance)” (pg. 169, para. 3), i.e., selecting at least one intermediate recurrent parent from the recipient parent group;
c) “Ha 2 (carried by [the] Chebec [cultivar])… confer[s] resistance to the Australian pathotype of [cereal cyst nematode]. Chebec was selected as the donor of CCN resistance in the backcross strategy” (pg. 148, para. 4), i.e., selecting a donor parent plant comprising the at least one agronomic trait of interest;
d) “backcross populations used… were developed from two recurrent parents… widely adapted to southern Australian cropping environments” (pg. 71, para. 5 – pg. 72, para. 1), i.e., a population of recipient parents into which at least one agronomic trait is to be introgressed; and
e) “BC1 populations were sown in adjacent field plot experiments… arranged as single replicate nurseries with alternating donor and recurrent parent check plots every fifth plot“ (pg. 154, para. 1), i.e., plants derived from at least one traited parent were planted in a growing space and directed into the genetic distance grouping procedure.
Jefferies does not explicitly disclose introgressing a trait from a recurrent parent to other recipient parents, however, this is merely an embodiment of the disclosed multi-round introgression process.
Jefferies discusses “using genetic distance estimates between parents as a tool for choosing… recurrent parents” (pg. 12, para. 2), but does not disclose selecting a recurrent parent that is centric in genetic distance relative to other members of a group.
Soleimani discusses “Collections of plant genetic resources stored in genebanks… an important source of genetic diversity for improvement in plant breeding programs”, and teaches application of “general clustering approaches… available to subdivide a large data set into small groups with maximum genetic diversity between groups” (pg. 1, Abstract).
Soleimani further teaches that “Germplasm collections… provide a source of novel traits for sustainable crop improvement… Originally, phenotypic data containing both morphological and agronomic traits were used to create core collections, whereas nowadays molecular markers as neutral tools for measuring genetic variation have become the tool of choice” (pg. 2, r. column).
Soleimani presents an experimental study wherein “genotypes were clustered into… groups by using the k-medoids clustering method” (pg. 4, l. column) wherein “K-medoids… minimiz[es] the distance between data points within a cluster to the respective cluster center… in k-medoids the cluster center needs to be a real object of the collection” (pg. 3, l. column).
Soleimani further presents method quality assessment wherein “genetic metrics were applied to assess the quality of different core set selection methods… For such an objective the average A-NE value should be as small as possible. An average A-NE value equal to zero indicates a minimal distance between genotypes… the k-medoids… core sets did the best job… with the lowest average value of A-NE observed” (pg. 7, l. column). In other words, the applied clustering method effectively groups a population, by genetic distance, such that each group comprises a member centric in genetic distance relative to other members of the group.
Additionally, Soleimani teaches that “These methods could be used to select genetically diverse genotypes for carrying out different scientific research before a large number of genotypes are phenotyped, thus excluding genotypes that would show the same behavior. Therefore, by eliminating the need for an additional phenotyping step, these approaches could accelerate… breeding programs” (pg. 6, r. column).
With respect to claim 12, Jefferies teaches that “For some traits, it is possible to select from a range of donor parents” (pg. 2, para. 2), and exemplifies a breeding process wherein “backcross populations used… were developed from two recurrent parents” (pg. 71, para. 5). Jefferies further discusses “a backcross breeding program to introgress stem rust resistance into 10 adapted Australian wheat cultivars”, wherein “[w]idely adapted cultivars including Insignia, Bencubbin and Dirk were chosen as recurrent parents” (pg. 7, para. 1). Jefferies thereby exemplifies selection of a plurality of recurrent parents.
Furthermore, the selection of a core collection of accessions having minimal within-cluster genetic distance, according to the k-medoids method taught by Soleimani (pg. 4, l. column), is considered equivalent to selection of a plurality of recurrent parents associated with a plurality of recipient groups as claimed.
With respect to claims 14-15, Jefferies exemplifies a breeding process wherein “The measure of distance among cultivars was the covariance of allele frequencies summed for all fragments scored. The genetic distance matrix was used for cluster analysis using the Unweighted Pair Group Method of Averages (UPGMA)” (pg. 155, para. 4 – pg. 156, para. 1), wherein “The most genetically different parents were the Algerian landrace Sahara and the Japanese malting quality cultivar, Amagi Nijo (GD = 0.139)” (pg. 156, para. 3), i.e., genetic distance of 13.9%. In other words, a genetic distance between any two members is ≤ 65%, and is ≤ 80%, according to identity by descent.
With respect to claim 16, Jefferies exemplifies a breeding process wherein “Four donor parents were chosen for the development of BC1 populations… BC1 F2 populations were created from crosses between the four donor parents and the recurrent parent” (pg. 152, paras. 2-3). Jefferies thereby exemplifies utilizing a group of parents comprising one recurrent parent and further comprising zero (≤10) other recipient parents. See In re Mochel, 470 F.2d 638, 176 USPQ 194 (CCPA 1974).
With respect to claim 17, Jefferies discloses techniques for “simultaneous selection for multiple traits” (pg. 21, para. 1), comprising “introgressing several traits in the single program… with the use of several backcross streams, introgressing each trait in a separate backcross stream and then merging the streams near or at the final cross… the major advantage would be in the selection [of] desirable recombinants for several traits almost simultaneously within the final merged population… if more than one marker linked trait is carried by a single donor parent… the traits can be selected simultaneously” (pg. 23, para. 4). Jefferies thus teaches a method utilizing multiple backcross streams, wherein given members of a single population are parents in multiple recipient groups.
With respect to claim 18, Jefferies teaches that “a plant breeder can improve genetic variability through; (1) choice of donor and recurrent parents based on estimates of genetic distance [and] (2) control of the number of backcrosses before selection” (pg. 3, para. 4). Jefferies further teaches that “In a survey of methodology used by wheat breeders throughout the world, Peterson (1957) found that many wheat breeders did not use the full backcross method to reconstitute the recurrent parent, but used only one, two or three backcrosses to retain the benefits of transgressive segregation for agronomic characters such as grain yield” (pg. 14, para. 4).
With respect to claim 20, Jefferies discloses “introgression of agronomically important traits” (pg. 2, para. 4), and exemplifies “agronomic traits to be considered… includ[ing] resistance to cereal cyst nematode (CCN) (Heterodera avenae), resistance to barley leaf scald (Rhyncosporium secali), [and] resistance to barley yellow dwarf virus (BYDV)” (pg. 2, para. 5), i.e., resistance to plant pathogens. Jefferies further discloses that “All marker analyses were performed with [a] computer program” (pg. 52, para. 5).
An invention would have been obvious to one of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, said practitioner would have implemented the k-medoids clustering method (and thereby grouped a population of parents such that at least one member is centric in genetic distance relative to other members of a group), as taught by Soleimani, to enhance the genetic distance-based introgression techniques of Jefferies, because Soleimani teaches that k-medoids clustering is an effective method of selecting plants having minimal genetic distance to other members of maximally diverse clusters within a population (pg. 3, l. column; pg. 7, l. column), and teaches that k-medoid clustering can exclude redundant genotypes and accelerate breeding programs (pg. 6, r. column). Said practitioner would have had a reasonable expectation of success because Jefferies and Soleimani both discuss methods of selecting optimal plant genotypes based on genetic distance analysis.
In this way the disclosure of Jefferies, in view of Soleimani, makes obvious the limitations of claims 1-8, 10-12, 14-18 and 20. Thus, the claimed invention is prima facie obvious.
Conclusion
At this point in prosecution, no claims are allowable.
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).
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/T.C.S./Examiner, Art Unit 1685
/JESSE P FRUMKIN/Primary Examiner, Art Unit 1685 June 16, 2026
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