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 .
Priority
Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e).
Status of the Claims
Claims 1-9 are pending.
Claims 1-9 are examined herein.
Specification
The disclosure is objected to because of the following informalities:
The Specification recites in multiple places the insertion polymorphism sequence CCCGAGTTACAA. This sequence comprises 12 contiguous specifically defined nucleotides and as such the recitation of the sequence must be accompanied by a sequence identifier. (See MPEP 1.831). In this case, the remedy does not require any alteration of the sequence listing as CCCGAGTTACAA is the sequence listed in the instant SEQ ID NO:3.
Appropriate correction is required.
Claim Objections
Claim 9 is objected to because of the following informalities:
Claim 9 recites the insertion polymorphism sequence CCCGAGTTACAA. This sequence comprises 12 contiguous specifically defined nucleotides and as such the recitation of the sequence must be accompanied by a sequence identifier. (See MPEP 1.831). In this case, the remedy does not require any alteration of the sequence listing as CCCGAGTTACAA is the sequence listed in the instant SEQ ID NO:3.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 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 6-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception – here a natural phenomenon - without significantly more. The claims recite a soybean plant comprising a marker associated with IDC resistance wherein the marker comprises a polymorphism identified by SEQ ID NO:1 and 2. This judicial exception is not integrated into a practical application because the rejected claims recite no application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the markers and plants appear in natural soybean populations as disclosed by Peiffer, Gregory A., et al. "Identification of candidate genes underlying an iron efficiency quantitative trait locus in soybean." Plant physiology 158.4 (2012): 1745-1754. Peiffer discloses the identification (detection) of a 12bp in-frame deletion in the Glyma03g28610 gene in soybean (a HLH transcription factor). Peiffer discloses that this deletion is in the gene that is the likely candidate for a QTL in soybean for iron use inefficiency which results in chlorosis. As such Peiffer discloses the deletion as a marker of iron deficiency chlorosis and the undeleted sequence as a marker for IDC resistance. (Abstract, p. 1747 right col. ¶ 3 – p. 1749 left col. ¶ 1, p. 1750 left col. ¶ 2). Peiffer discloses that the deletion is at position 36552946 on Chromosome 3, which corresponds exactly to the position of the 12bp deletion in the instant claims. Peiffer discloses that the sequence that was deleted encodes the amino acids PELQ and because this is the sequence encoded by the instantly identified marker sequence of CCCGAGTTACAA (SEQ ID NO:3), it is reasonable to conclude that the deletion identified by Peiffer is the same deletion sequence that is the subject of the instant claims. (p. 1750 left col. ¶ 2). As such the markers and plants are natural phenomenon and the claims are directed to ineligible subject matter.
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 1,2,6 and 7 are 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 recites “A method of determining the genotype of a soybean plant, wherein said method comprises obtaining a sample of nucleic acids from the soybean plant and detecting in the nucleic acids, a plurality of polymorphisms, wherein said plurality of polymorphisms correspond to the nucleotide polymorphisms identified in any one or more of SEQ ID NOs: 1-2”.
Claim 2 recites “A method for developing an Iron Deficiency Chlorosis resistant soybean plant, wherein the method comprises applying marker enhanced selection to detect one or more polymorphisms, wherein said one or more polymorphisms are selected from the nucleotide polymorphisms in any one or more of SEQ ID NOs: 1-2.”
It is unclear what the “plurality of polymorphisms” or “one or more polymorphisms” means with respect to “polymorphisms identified in any one or more of SEQ ID NOs: 1-2” or “polymorphisms in any one or more of SEQ ID NOs: 1-2”. There is a single difference between SEQ ID NO:1 and SEQ ID NO:2 – a 12 nucleotide deletion. It is unclear if the “plurality of polymorphisms” means other polymorphisms that are not described by the instant disclosure or something else. The claims require both that there are more than one polymorphism but also require that they are somehow identified by SEQ ID NO:1 and 2, which identify only one polymorphism. The claims are internally contradictory. As such, the metes and bounds of the claims are unclear.
For purposes of applying prior art, the “plurality of polymorphisms” is interpreted to mean the 12 bp deletion between SEQ ID NO:1 and 2. This interpretation does not relieve applicant of the duty to amend the claims to address the cited deficiency.
Claim 6 recites “A soybean plant having in its genome, a chromosomal interval, wherein the chromosomal interval comprises detection of resistance to Iron Deficiency Chlorosis beginning at about base pair 36,552,796 and ending at about base pair 36,553,107 on chromosome 3 of the Williams82a2.75 reference genome or equivalent thereof in other Glycine max lines.” The term “wherein the chromosomal interval comprises detection of resistance to Iron Deficiency Chlorosis” is unclear. Chromosome intervals do not appear to be capable of anything like “detection: As such, the metes and bounds of the claim are unclear. For purposes of applying art, the claim in interpreted to mean that the soybean plant comprises a sequence associated with IDC resistance at or about the recited position (corresponding to the instant SEQ ID NO:1 and 2). This interpretation does not relieve applicant of the duty to amend the claims to address the cited deficiency.
Claim 7 recites “The plant of any one of claims 7, wherein the chromosome interval comprises:a. Any one or more of SEQ ID NOs:1-2 or any portion thereof, conferring resistance to Iron Deficiency Chlorosis; or b. A InDel marker associated with increased resistance to Iron Deficiency Chlorosis, wherein said marker corresponds with any one of the markers from any one or more of SEQ ID NO:1-2.” Claim 7 depends from itself and as such it both lacks antecedent basis and is improperly dependent. For purposes of examination Claim 7 is interpreted to be dependent from Claim 6, which at least recites a chromosome interval. This interpretation does not relieve applicant of the duty to amend the claims to address the cited deficiency.
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2 and 6-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Peiffer, Gregory A., et al. "Identification of candidate genes underlying an iron efficiency quantitative trait locus in soybean." Plant physiology 158.4 (2012): 1745-1754.
Applicant claims as follows:
A method of determining the genotype of a soybean plant, wherein said method comprises obtaining a sample of nucleic acids from the soybean plant and detecting in the nucleic acids,a plurality of polymorphisms, wherein said plurality of polymorphisms correspond to the nucleotide polymorphisms identified in any one or more of SEQ ID NOs: 1-2.
A method for developing an Iron Deficiency Chlorosis resistant soybean plant, wherein the method comprises applying marker enhanced selection to detect one or more polymorphisms, wherein said one or more polymorphisms are selected from the nucleotide polymorphisms in any one or more of SEQ ID NOs: 1-2.
A soybean plant having in its genome, a chromosomal interval, wherein the chromosomal interval comprises detection of resistance to Iron Deficiency Chlorosis beginning at about base pair 36,552,796 and ending at about base pair 36,553,107 on chromosome 3 of the Williams82a2.75 reference genome or equivalent thereof in other Glycine max lines.
The plant of any one of claims 7 (see 112(b) rejection), wherein the chromosome interval comprises: a. Any one or more of SEQ ID NOs:1-2 or any portion thereof, conferring resistance to Iron Deficiency Chlorosis; or b. A InDel marker associated with increased resistance to Iron Deficiency Chlorosis, wherein said marker corresponds with any one of the markers from any one or more of SEQ ID NO:1-2.
A marker for detecting resistance to Iron Deficiency Chlorosis, wherein said marker comprises a polymorphism relative to a reference soybean genome for Glycine max at nucleotide position 36,552,946 on chromosome 3, wherein the reference genome is the Glycine max Williams82a2.75 reference genome.
A marker for detecting resistance to Iron Deficiency Chlorosis, wherein said marker comprises a nucleotide position comprising a polymorphism on soybean chromosome 3 relative to a reference soybean genome of a CCCGAGTTACAA insertion genotype at position 36,552,946, wherein the reference genome is the Glycine max Williams82a2.75 reference genome.
Peiffer discloses the identification (detection) of a 12bp in-frame deletion in the Glyma03g28610 gene in soybean (a HLH transcription factor). Peiffer discloses that this deletion is in the gene that is the likely candidate for a QTL in soybean for iron use inefficiency which results in chlorosis. As such Peiffer discloses the deletion as a marker of iron deficiency chlorosis and the undeleted sequence as a marker for IDC resistance. (Abstract, p. 1747 right col. ¶ 3 – p. 1749 left col. ¶ 1, p. 1750 left col. ¶ 2). Peiffer discloses that the deletion is at position 36552946 on Chromosome 3, which corresponds exactly to the position of the 12bp deletion in the instant claims. Peiffer discloses that the sequence that was deleted encodes the amino acids PELQ and because this is the sequence encoded by the instantly identified marker sequence of CCCGAGTTACAA (SEQ ID NO:3), it is reasonable to conclude that the deletion identified by Peiffer is the same deletion sequence that is the subject of the instant claims. (p. 1750 left col. ¶ 2).
As such, the claimed inventions are anticipated by the disclosures of the prior art.
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 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 of this title, 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.
Claims 3-5 are rejected under 35 U.S.C. 103 as being unpatentable over Peiffer, Gregory A., et al. "Identification of candidate genes underlying an iron efficiency quantitative trait locus in soybean." Plant physiology 158.4 (2012): 1745-1754.
A method of producing a soybean plant that has improved resistance to Iron Deficiency Chlorosis as compared to a control plant, wherein the method comprises:a. Isolating a nucleic acid from a soybean plant;b. Detecting in the nucleic acid, the presence of a genetic marker that is associated with improved resistance to Iron Deficiency Chiorosis, wherein said genetic marker is selected from any one or more of SEQ ID NOs: 1-2;c. Selecting a first soybean plant based on the presence of the marker associated with improved resistance;d. Crossing a second soybean plant with said first soybean plant, wherein the second soybean plant does not comprise in its genome the marker associated with improved resistance to Iron Deficiency Chlorosis;e. Producing seed from said crossing; and f. Selecting a soybean plant grown from said seed that has improved resistance to Iron Deficiency Chlorosis and comprises the genetic marker associated with improved resistance to Iron Deficiency Chlorosis.
The method of claim 3, further comprising the step of backcrossing the plants produced from step (f).
A soybean plant produced by the method of claim 3, wherein the plant comprises the genetic marker associated with improved resistance to Iron Deficiency Chlorosis.
The disclosures of Peiffer are set forth previously herein. Peiffer further teaches introgression (crossing and backcrossing) of soybean lines that comprise both the IDC resistant and IDC susceptible soybean lines for mapping purposes. The resultant progeny were mapped using molecular markers at known positions to identify the trait locus (QTL) for IDC resistance and then backcrossed again for fine-mapping purposes. The progeny plants were scored for IDC phenotypes using a visual chlorosis scale. (p. 1752 right col. ¶ 3 – p. 1753 left col. ¶ 2).
Peiffer does not disclose the claimed inventions as a single embodiment and as such the claims are not rejected under 35 USC 102(a)(1). However, the combined teachings of Peiffer render the claimed inventions obvious.
It would have been prima facie obvious at the time of filing for one of ordinary skill in the art to modify the processes of Peiffer to arrive at Applicant’s claimed processes and product plants. One having ordinary skill would have been motivated to do so because Peiffer teaches that the 12bp deletion is a confirmed marker that correlates to IDC susceptibility and the presence of the 12bp confers IDC resistance. As such it is not only a marker that correlates at 100% for the agronomically desirable phenotype of IDC resistance, but the deletion is also predicted by Peiffer to structurally alter the binding capabilities of the encoded protein such that function would be disrupted. The marker therefor probably resides in the gene that is the responsible for the IDC phenotypes. Peiffer teaches all of the recited process steps of crossing, detecting markers and selecting and backcrossing soybean plants. As such it would have been prima facie obvious to cross the plants with IDC resistance into elite soybean lines that lack this useful trait, detect the identified polymorphism and then further backcross the plant lines to arrive at plants that have the otherwise desirable traits of the recurrent parent and the IDC resistance allele with minimal other DNA from the donor parent.
As such, the claimed inventions are obvious in view of the teachings of the prior art.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHARLES A LOGSDON whose telephone number is (571)270-0282. The examiner can normally be reached M-F 8:30 - 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
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