IP Library Granted Patent US 12,305,175
Granted Patent B2
US 12,305,175 · App. 18/057,860 · Granted May 20, 2025

Modified excisable DAS68416-4 soybean transgenic herbicide resistance locus

Inventors: Michael Andreas Kock (Rheinfelden, DE); Joshua L. Price (Cambridge, MA); Michael Lee Nuccio (Salem, NH)
Assignee: INARI AGRICULTURE TECHNOLOGY, INC.
C12N15/8201A01H1/02A01H5/10A01H6/4684A01H6/542C07K14/415C12N9/22C12N15/11C12N15/8213C12N15/8286C12Q1/6834C12Q1/6895C12N2310/20C12N2800/80C12Q2600/13C12Q2600/156C12Q2600/158
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Quick Facts
Patent No.
US 12,305,175
App. No.
18/057,860
Granted
May 20, 2025
Kind
B2
Abstract

Transgenic INHT27 soybean plants comprising modifications of the DAS68416-4 soybean locus which provide for facile excision of the modified DAS68416-4 transgenic locus or portions thereof, methods of making such plants, and use of such plants to facilitate breeding are disclosed.

Claims (14)

1. A transgenic soybean plant cell comprising an INHT27 transgenic locus comprising the DNA molecule set forth in SEQ ID NO: 3.

2. A transgenic soybean plant part comprising the soybean plant cell of claim 1 .

3. The transgenic soybean plant part of claim 2 , wherein said soybean plant part is a seed.

4. A transgenic soybean plant comprising the soybean plant cell of claim 1 .

5. A method for obtaining a bulked population of inbred seed comprising selfing the transgenic soybean plant of claim 4 and harvesting seed comprising the INHT27 transgenic locus from the selfed soybean plant.

6. A method of obtaining hybrid soybean seed comprising crossing the transgenic soybean plant of claim 4 to a second soybean plant which is genetically distinct from the first soybean plant and harvesting seed comprising the INHT27 transgenic locus from the cross.

7. A DNA molecule comprising SEQ ID NO: 3.

8. A processed transgenic soybean plant product comprising the DNA molecule of claim 7 .

9. A biological sample containing the DNA molecule of claim 7 .

10. A method of detecting a soybean plant cell comprising the INHT27 transgenic locus of claim 1 , comprising the step of detecting a DNA molecule comprising SEQ ID NO: 9.

11. A method of excising the INHT 27 transgenic locus from the genome of the soybean plant cell of claim 1 , comprising the steps of:

(a) contacting the INHT 27 transgenic locus of the soybean plant cell with: (i) a Cas 12 a RNA dependent DNA endonuclease (RdDe); and (ii) a guide RNA (gRNA) capable of hybridizing to the guide RNA hybridization site of the originator guide RNA recognition site (OgRRS) and the cognate guide RNA recognition site (CgRRS) of SEQ ID NO: 3; wherein the Cas 12 a RdDe recognizes a OgRRS/gRNA and a CgRRS/gRNA hybridization complex; and,

(b) selecting a transgenic plant cell, transgenic plant part, or transgenic plant wherein the INHT 27 transgenic locus flanked by the OgRRS and the CgRRS has been excised.

12. The method of claim 11 , wherein said guide RNA comprises an RNA sequence encoded by SEQ ID NO: 13.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Dec 15, 2022
From: KOCK, MICHAEL ANDREAS; PRICE, JOSHUA L.; NUCCIO, MICHAEL LEE
To: INARI AGRICULTURE TECHNOLOGY, INC.
Reel/Frame 062100/0551 →
Continuity (13)
Continuation PCTUS2021043945 · Jul 30, 2021
Provisional Application 63203137 · Jul 9, 2021
Provisional Application 63202569 · Jun 16, 2021
Provisional Application 63201030 · Apr 9, 2021
Provisional Application 63201029 · Apr 9, 2021
Provisional Application 63199951 · Feb 4, 2021
Provisional Application 63199949 · Feb 4, 2021
Provisional Application 63199930 · Feb 3, 2021
Provisional Application 63059860 · Jul 31, 2020
Provisional Application 63059813 · Jul 31, 2020
Provisional Application 63059916 · Jul 31, 2020
Provisional Application 63059963 · Jul 31, 2020
Related Publication 20230087222A1 · Mar 23, 2023
References Cited (144)
US 7632985B2 · Malven et al. · 2009 [cited by applicant]
US 8232456B2 · Long et al. · 2012 [cited by applicant]
US 8450561B2 · Beazley et al. · 2013 [cited by applicant]
US 8455720B2 · Long et al. · 2013 [cited by applicant]
US 8575434B2 · Diehn et al. · 2013 [cited by applicant]
US 8680363B2 · Bard et al. · 2014 [cited by applicant]
US 9447428B2 · Brinker et al. · 2016 [cited by applicant]
US 9540655B2 · Cui et al. · 2017 [cited by applicant]
US 9738904B2 · Cui et al. · 2017 [cited by applicant]
US 9944944B2 · Cui · 2018 [cited by examiner]
US 11041172B2 · Cermak · 2021 [cited by applicant]
US 11214811B1 · Nuccio et al. · 2022 [cited by applicant]
US 11242534B1 · Nuccio et al. · 2022 [cited by applicant]
US 11326177B2 · Price et al. · 2022 [cited by applicant]
US 11359210B2 · Price et al. · 2022 [cited by applicant]
US 20030088081A1 · Maliga et al. · 2003 [cited by applicant]
US 20100162428A1 · Brown et al. · 2010 [cited by applicant]
US 20110191899A1 · Ainley et al. · 2011 [cited by applicant]
US 20130212747A1 · Cui et al. · 2013 [cited by applicant]
US 20130296170A1 · Hanger et al. · 2013 [cited by applicant]
US 20130324408A1 · Cui et al. · 2013 [cited by applicant]
US 20140041083A1 · Cui et al. · 2014 [cited by applicant]
US 20150059010A1 · Cigan et al. · 2015 [cited by applicant]
US 20150082478A1 · Cigan et al. · 2015 [cited by applicant]
US 20160029631A1 · Hellwege et al. · 2016 [cited by applicant]
US 20160333363A1 · Srivastava · 2016 [cited by applicant]
US 20170166912A1 · Brower-Toland et al. · 2017 [cited by applicant]
US 20180163218A1 · Corbin et al. · 2018 [cited by applicant]
US 20190112614A1 · Russell et al. · 2019 [cited by applicant]
US 20190136249A1 · Sakai et al. · 2019 [cited by applicant]
US 20190284644A1 · Mackenzie et al. · 2019 [cited by applicant]
US 20190320607A1 · Christensen et al. · 2019 [cited by applicant]
US 20190352655A1 · Niu et al. · 2019 [cited by applicant]
US 20200157554A1 · Cigan et al. · 2020 [cited by applicant]
US 20200208172A1 · Ikeda et al. · 2020 [cited by applicant]
US 20200405649A1 · Wang et al. · 2020 [cited by applicant]
US 20220030806A1 · Price et al. · 2022 [cited by applicant]
US 20220030822A1 · Nuccio et al. · 2022 [cited by applicant]
US 20220033833A1 · Gilbertson et al. · 2022 [cited by applicant]
US 20220098602A1 · Nuccio et al. · 2022 [cited by applicant]
US 20220154194A1 · Nuccio et al. · 2022 [cited by applicant]
US 20220251584A1 · Nuccio et al. · 2022 [cited by applicant]
US 20220364105A1 · Price et al. · 2022 [cited by applicant]
US 20230022576A1 · Sheva · 2023 [cited by applicant]
US 20230077473A1 · Price et al. · 2023 [cited by applicant]
US 20230078387A1 · Kock et al. · 2023 [cited by applicant]
US 20230083144A1 · Nuccio et al. · 2023 [cited by applicant]
US 20230147013A1 · Nuccio et al. · 2023 [cited by applicant]
US 20230203514A1 · Price et al. · 2023 [cited by applicant]
US 20230265445A1 · Kock et al. · 2023 [cited by applicant]
US 20240011042A1 · Kock et al. · 2024 [cited by applicant]
WO WO2011091311A2 · 2011 [cited by examiner]
WO 2022026375A1 · 2022 [cited by applicant]
WO 2022026379A1 · 2022 [cited by applicant]
WO 2022026390A1 · 2022 [cited by applicant]
WO 2022026395A2 · 2022 [cited by applicant]
WO 2022026403A2 · 2022 [cited by applicant]
WO 2022026540A1 · 2022 [cited by applicant]
WO 2022026801A1 · 2022 [cited by applicant]
Meriam Webster dictionary (Variant Definition & Meaning—Merriam-Webster). https://www.merriam-webster.com/dictionary/variant, accessed May 23, 2023. (Year: 2023). [cited by examiner]
Zhang et al., 2015, Off-target effects in CRISPR/Cas9-mediated genome engineering. Molecular Therapy-Nucleic Acids, 4, e264. (Year: 2015). [cited by examiner]
Zhong et al., 2018, Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Molecular plant, 11(7), 999-1002. (Year: 2018). [cited by examiner]
Li et al., 2018, Expanding the scope of CRISPR/Cpf1-mediated genome editing in rice. Molecular Plant, 11(7), 995-998. (Year: 2018). [cited by examiner]
Bagemann et al., 2017, Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Scientific reports, 7(1), 11606. (Year: 2017). [cited by examiner]
Bagemann et al., 2017, Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases (Supplementary Data). Scientific reports, 7(1), 11606. (Year: 2017). [cited by examiner]
Zhong et al., 2018, Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites (Supplementary Data). Molecular plant, 11(7), 999-1002. (Year: 2018). [cited by examiner]
Finnigan et al. 2016. mCAL: a new approach for versatile multiplex action of Cas9 using one sgRNA and loci flanked by a programmed target sequence. G3: Genes, Genomes, Genetics, 6(7), 2147-2156 (reference Publication, s… [cited by examiner]
Specht et al., 2020, Massively parallel CRISPRi assays reveal concealed thermodynamic determinants of dCas12a binding. Proceedings of the National Academy of Sciences, 117(21), 11274-11282. (Year: 2020). [cited by examiner]
Baliga et al., “Investigation of direct repeats, spacers and proteins associated with clustered regularly interspaced short palindromic repeat (CRISPR) system of Vibrio parahaemolyticus,” Molecular Genetics and Genomics… [cited by applicant]
Biopesticides Registration Action Document, “Bacillus thuringiensis Vip3Aa20 Insecticidal Protein and the Genetic Material Necessary for Its Production (via Elements of Vector pNOV1300) in Event MIR162 Maize (OECD Uniqu… [cited by applicant]
Bissler, J.J., “Triplex DNA and human disease,” Frontiers in Bioscience, May 1, 2007, vol. 12, pp. 4536-4546. [cited by applicant]
Bortesi et al., “The CRISPR/Cas9 system for plant genome editing and beyond,” Biotechnology Advances, Dec. 20, 2014, vol. 33, Issue 1, pp. 41-52. [cited by applicant]
Charpentier et al., “Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity,” FEMS Microbiology Reviews, May 19, 2015, vol. 39, Issue 3, pp. 428-441. [cited by applicant]
Cho et al., “Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus,” Plant Direct, vol. 3, Aug. 27, 2019, 16 pages. [cited by applicant]
Du et al., “Construction of Marker-Free Genetically Modified Maize Using a Heat-Inducible Auto-Excision Vector,” Genes, May 17, 2019, vol. 10, No. 374, 17 pages. [cited by applicant]
Du et al., “Infection of Embryonic Callus with Agrobacterium Enables High-Speed Transformation of Maize,” International Journal of Molecular Sciences, Jan. 11, 2019, vol. 20, No. 279, 15 pages. [cited by applicant]
Finnigan et al., “mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence,” G3: Genes, Genomes, Genetics, Jul. 1, 2016, vol. 6, pp. 2147-2156. [cited by applicant]
Gurusaran et al., “RepEx: Repeat extractor for biological sequences,” Genomics, Jul. 21, 2013, vol. 102, pp. 403-408. [cited by applicant]
International Searching Authority in connection with PCT/US21/43897 filed Jul. 30, 2021, “Invitation to Pay Additional Fees And, Where Applicable, Protest Fee,” mailed Oct. 27, 2021, 3 pages. [cited by applicant]
International Searching Authority in connection with PCT/US21/43935 filed Jul. 30, 2021, “Invitation to Pay Additional Fees And, Where Applicable, Protest Fee,” mailed Oct. 26, 2021, 3 pages. [cited by applicant]
International Searching Authority in connection with PCT/US21/43945 filed Jul. 30, 2021, “Invitation to Pay Additional Fees And, Where Applicable, Protest Fee,” mailed Oct. 27, 2021, 3 pages. [cited by applicant]
Kim et al., “CRISPR/Cpf1-mediated DNA-free plant genome editing,” Nature Communications, Feb. 16, 2017, vol. 8, Article No. 14406, 7 pages. [cited by applicant]
Li et al., “Expanding the Scope of CRISPR/Cpf1-Mediated Genome Editing in Rice,” Molecular Plant, Jul. 2, 2018, vol. 11, No. 7, pp. 995-998, 14 pages. [cited by applicant]
Luo et al., “Improperly Terminated, Unpolyadenylated mRNA of Sense Transgenes is Targeted by RDR6-Mediated RNA Silencing in [cited by applicant]
Malzahn et al., “Application of CRISPR-Casl 2a temperature sensitivity for improved genome editing in rice, maize, and [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/248,936, mailed Mar. 25, 2021, 25 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/249,640, mailed Jun. 29, 2021, 10 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/302,110, mailed Jun. 29, 2021, 22 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/302,121, mailed Jul. 8, 2021, 10 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/302,739, mailed Aug. 3, 2021, 24 pages. [cited by applicant]
Que et al., “Maize transformation technology development for commercial event generation,” Frontiers in Plant Science, Aug. 5, 2014, vol. 5, Article No. 379, 19 pages. [cited by applicant]
Srivastava et al., “Gene Stacking by recombinases,” Plant Biotechnology Journal, Feb. 2016, vol. 14, pp. 471-482. [cited by applicant]
Srivastava, et al., “Dual-targeting by CRISPR/Cas9 for precise excision of transgenes from rice genome,” Plant Cell Tissue and Organ Culture, Jan. 20, 2017, vol. 129, pp. 153-160. [cited by applicant]
Ward et al., “Petition for Determination of Nonregulated Status for Insect-Resistant MIR162 Maize,” Syngenta Biotechnology, Inc., Aug. 31, 2007, 271 pages. [cited by applicant]
“What is a CRISPR-Cas system?,” CRISPR-CAS++, Universite Paris-Saclay, accessed Nov. 2, 2021. Retrieved from the Internet <URL:https://crisprcas.i2bc.paris-saclay.fr/Home/About>, 2 pages. [cited by applicant]
Xing et al., “Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminators,” Plant Biotechnology Journal, Sep. 2010, vol. 8, pp. 772-782. [cited by applicant]
Young et al., “CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement,” Scientific Reports, Apr. 30, 2019, vol. 9, No. 6729, 11 pages. [cited by applicant]
Danilo et al., “The DFR locus: A smart landing pad for targeted transgene insertion in tomato,” PLoS One, Dec. 6, 2018, vol. 13, No. 12, pp. 1-14. [cited by applicant]
Gleditzsch et al., “PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures,” RNA Biology, Apr. 2019, vol. 16, No. 4, pp. 504-517. [cited by applicant]
International Search Report in PCT/US2021/043161, mailed Jan. 5, 2022, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/043170, mailed Jan. 5, 2022, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/043187, mailed Jan. 6, 2022, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/043192, mailed Jan. 27, 2022, 7 pages. [cited by applicant]
International Search Report in PCT/US2021/043207, mailed Jan. 27, 2022, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/043440, mailed Dec. 2, 2021, 3 pages. [cited by applicant]
International Search Report in PCT/US2021/043468, mailed Nov. 26, 2021, 4 pages. [cited by applicant]
International Search Report in PCT/US2021/043479, mailed Nov. 23, 2021, 3 pages. [cited by applicant]
International Search Report in PCT/US2021/043483, mailed Dec. 16, 2021, 3 pages. [cited by applicant]
International Search Report in PCT/US2021/043496, mailed Dec. 1, 2021, 4 pages. [cited by applicant]
International Search Report in PCT/US2021/043851, mailed Dec. 30, 2021, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/043919, mailed Jan. 20, 2022, 8 pages. [cited by applicant]
International Search Report in PCT/US2021/043933, mailed Dec. 30, 2021, 6 pages. [cited by applicant]
International Search Report in PCT/US2021/044198, mailed Jan. 19, 2022, 6 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/302,110, mailed May 24, 2023, 27 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/650,031, mailed May 26, 2023, 11 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/680,647, mailed Jun. 23, 2023, 11 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/057,867, mailed Jun. 7, 2023, 17 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/058,081, mailed Apr. 11, 2023, 19 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/058,144, mailed Jun. 7, 2023, 49 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/058,156, mailed May 19, 2023, 24 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/058,161, mailed Apr. 11, 2023, 15 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/162,134, mailed Jun. 21, 2023, 28 pages. [cited by applicant]
Notice of Allowance in U.S. Appl. No. 17/248,936, mailed Mar. 10, 2022, 7 pages. [cited by applicant]
Notice of Allowance in U.S. Appl. No. 17/249,640, mailed Sep. 22, 2021, 7 pages. [cited by applicant]
Notice of Allowance in U.S. Appl. No. 17/302,121, mailed Nov. 15, 2021, 7 pages. [cited by applicant]
Notice of Allowance in U.S. Appl. No. 17/302,739, mailed Mar. 30, 2022, 7 pages. [cited by applicant]
Notice of Allowance in U.S. Appl. No. 17/680,647, mailed Apr. 27, 2023, 7 pages. [cited by applicant]
Rudgers et al., “EXZACTTM Precision Technology: Scientific and Regulatory Advancements in Plant-Genome Editing with ZFNs,” NABC, 2014, pp. 113-124. [cited by applicant]
Shi et al., “ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions,” Plant Biotechnology Journal, Feb. 2017, vol. 15, pp. 207-216. [cited by applicant]
Yau et al.,“Less is more: strategies to remove marker genes from transgenic plants,” BMC Biotechnology, Apr. 2013, vol. 13, No. 36, pp. 1-23. [cited by applicant]
GenBank Accession No. CP0049894, “Arachis ipaensis cultivar K30076 chromosome 03,” Jun. 3, 2020, https://www.ncbi.nlm.nih.gov/nuccore/CP049894, 2 pages. [cited by applicant]
International Search Report and Written Opinion in PCT/US2021/043897, mailed Feb. 10, 2022, 12 pages. [cited by applicant]
International Search Report and Written Opinion in PCT/US2021/043935, mailed Jan. 6, 2022, 13 pages. [cited by applicant]
International Search Report and Written Opinion in PCT/US2021/043945, mailed Jan. 21, 2022, 15 pages. [cited by applicant]
Li et al. Expanding the scope of CRISPR/Cpf1-mediated genome editing in rice; Molecular Plant 11:995-998, 2018, Supplemental Data, p. 1-10. [cited by applicant]
Ali et al., “Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice,” Communications Biology, vol. 3, Jan. 2020, 13 pages. [cited by applicant]
Bernabe-Orts et al., “Assessment of Cas12a-mediated gene editing efficiency in plants,” Plant Biotechnology Journal, vol. 17, No. 10, 2019, pp. 1971-1984. [cited by applicant]
Cai et al., “Broadening the targetable space: engineering and discovery of PAM-flexible Cas proteins,” Trends in Microbiology, May 2024, 4 pages. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 17/302,110, mailed Oct. 16, 2024, 24 pages. [cited by applicant]
Extended European Search Report in EP21849192.6, mailed Aug. 30, 2024, 17 pages. [cited by applicant]
Lee et al., “Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize,” Plant Biotechnology Journal, vol. 17, No. 2, 2019, pp. 362-372. [cited by applicant]
Non-Final Office Action in U.S. Appl. No. 18/162,134, mailed Sep. 26, 2024, 27 pages. [cited by applicant]
Wang et al., “Generation of marker-free transgenic rice using CRISPR/Cas9 system controlled by floral specific promoters,” Journal of Genetics and Genomics, vol. 46, 2019, pp. 61-64. [cited by applicant]
“Requirement for Unity of Invention” cited in U.S. Appl. No. 18/007,001, filed Jan. 26, 2023, 8 pages, mailed Jan. 27, 2025. [cited by applicant]