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Schreiber T, Prange A, Schäfer P, Iwen T, Grützner R, Marillonnet S, Lepage A, Javelle M, Paul W, Tissier A. Efficient scar-free knock-ins of several kilobases in plants by engineered CRISPR-Cas endonucleases. MOLECULAR PLANT 2024; 17:824-837. [PMID: 38520090 DOI: 10.1016/j.molp.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
In plants and mammals, non-homologous end-joining is the dominant pathway to repair DNA double-strand breaks, making it challenging to generate knock-in events. In this study, we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana. We achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation systems. In Arabidopsis thaliana, fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of transformants. In addition, we demonstrated stable and heritable knock-ins in wheat in 1% of the primary transformants. Taken together, our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.
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Affiliation(s)
- Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Anja Prange
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Petra Schäfer
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Thomas Iwen
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Ramona Grützner
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Aurélie Lepage
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Marie Javelle
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Wyatt Paul
- Limagrain, Centre de Recherche, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany.
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2
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Capdeville N, Schindele P, Puchta H. Increasing deletion sizes and the efficiency of CRISPR/Cas9-mediated mutagenesis by SunTag-mediated TREX1 recruitment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:277-287. [PMID: 38113345 DOI: 10.1111/tpj.16586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Previously, it has been shown that mutagenesis frequencies can be improved by directly fusing the human exonuclease TREX2 to Cas9, resulting in a strong increase in the frequency of smaller deletions at the cut site. Here, we demonstrate that, by using the SunTag system for recruitment of TREX2, the mutagenesis efficiency can be doubled in comparison to the direct fusion in Arabidopsis thaliana. Therefore, we also tested the efficiency of the system for targeted deletion formation by recruiting two other 3'-5' exonucleases, namely the human TREX1 and E. coli ExoI. It turns out that SunTag-mediated recruitment of TREX1 not only improved the general mutation induction efficiency slightly in comparison to TREX2, but that, more importantly, the mean size of the induced deletions was also enhanced, mainly via an increase of deletions of 25 bp or more. EcExoI also yielded a higher amount of larger deletions. However, only in the case of TREX1 and TREX2, the effect was predominately SunTag-dependent, indicating efficient target-specific recruitment. Using SunTag-mediated TREX1 recruitment at other genomic sites, we were able to obtain similar deletion patterns. Thus, we were able to develop an attractive novel editing tool that is especially useful for obtaining deletions in the range from 20 to 40 bp around the cut site. Such sizes are often required for the manipulation of cis-regulatory elements. This feature is closing an existing gap as previous approaches, based on single nucleases or paired nickases or nucleases, resulted in either shorter or longer deletions, respectively.
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Affiliation(s)
- Niklas Capdeville
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Patrick Schindele
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Holger Puchta
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
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3
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Liu D, Myers EA, Xuan S, Prichard LE, Donahue LI, Ellison EE, Starker CG, Voytas DF. Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs. PLANT PHYSIOLOGY 2024; 194:2229-2239. [PMID: 38243587 DOI: 10.1093/plphys/kiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.
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Affiliation(s)
- Degao Liu
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erik A Myers
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Shuya Xuan
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lynn E Prichard
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lilee I Donahue
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
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4
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Guirguis A, Yang W, Conlan XA, Kong L, Cahill DM, Wang Y. Boosting Plant Photosynthesis with Carbon Dots: A Critical Review of Performance and Prospects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300671. [PMID: 37381636 DOI: 10.1002/smll.202300671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/31/2023] [Indexed: 06/30/2023]
Abstract
Artificially augmented photosynthesis in nano-bionic plants requires tunable nano-antenna structures with physiochemical and optoelectronic properties, as well as unique light conversion capabilities. The use of nanomaterials to promote light capture across photosystems, primarily by carbon dots, has shown promising results in enhancing photosynthesis through tunable uptake, translocation, and biocompatibility. Carbon dots possess the ability to perform both down and up-light conversions, making them effective light promoters for harnessing solar energy beyond visible light wavelengths.This review presents and discusses the recent progress in fabrication, chemistry, and morphology, as well as other properties such as photoluminescence and energy conversion efficiency of nano-antennas based on carbon dots. The performance of artificially boosted photosynthesis is discussed and then correlated with the conversion properties of carbon dots and how they are applied to plant models. The challenges related to the nanomaterial delivery and the performance evaluation practices in modified photosystems, consideration of the reliability of this approach, and the potential avenues for performance improvements through other types of nano-antennas based on alternative nanomaterials are also critically evaluated. It is anticipated that this review will stimulate more high-quality research in plant nano-bionics and provide avenues to enhance photosynthesis for future agricultural applications.
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Affiliation(s)
- Albert Guirguis
- School of Life & Environment Sciences, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Wenrong Yang
- School of Life & Environment Sciences, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Xavier A Conlan
- School of Life & Environment Sciences, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - David M Cahill
- School of Life & Environment Sciences, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Yichao Wang
- School of Life & Environment Sciences, Deakin University, Waurn Ponds, Victoria, 3216, Australia
- School of Engineering, Design and Built Environment, Western Sydney University, Penrith, NSW, 2751, Australia
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Yuan G, Liu Y, Yao T, Muchero W, Chen JG, Tuskan GA, Yang X. eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone '52-225'. PLANTS (BASEL, SWITZERLAND) 2023; 12:1657. [PMID: 37111880 PMCID: PMC10145771 DOI: 10.3390/plants12081657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone '52-225' (P. trichocarpa × P. deltoides clone '52-225'). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.
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Affiliation(s)
- Guoliang Yuan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Yang Liu
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
| | - Tao Yao
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Myers ZA, Wootan CM, Liang Z, Zhou P, Engelhorn J, Hartwig T, Nathan SM. Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis. PLANT DIRECT 2023; 7:e489. [PMID: 37124872 PMCID: PMC10133983 DOI: 10.1002/pld3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 05/03/2023]
Abstract
The Heat Shock Factor (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess and compare the composition, heat responsiveness, and chromatin profiles of the HSF families in maize and Setaria viridis (Setaria), two model C4 panicoid grasses. Both species encode a similar number of HSFs, and examples of both conserved and variable expression responses to a heat stress event were observed between the two species. Chromatin accessibility and genome-wide DNA-binding profiles were generated to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both chromatin accessibility and promoter occupancy within similarly regulated sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. Additionally, we observed the widespread presence of TF binding at HSF promoters in control conditions, even at HSFs that are only expressed in response to heat stress. TF-binding peaks were typically near putative HSF-binding sites in HSFs upregulated in response to heat stress, but not in stable or not expressed HSFs. These observations collectively support a complex scenario of expansion and subfunctionalization within this transcription factor family and suggest that within-family HSF transcriptional regulation is a conserved, defining feature of the family.
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Affiliation(s)
- Zachary A. Myers
- Department of Plant and Microbial BiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Clair M. Wootan
- Department of Plant and Microbial BiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Zhikai Liang
- Department of Plant and Microbial BiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Peng Zhou
- Chinese Academy of Agricultural SciencesInstitute of Crop SciencesBeijingChina
| | - Julia Engelhorn
- Heinrich‐Heine UniversityDüsseldorfGermany
- Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Thomas Hartwig
- Heinrich‐Heine UniversityDüsseldorfGermany
- Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Springer M. Nathan
- Department of Plant and Microbial BiologyUniversity of MinnesotaMinneapolisMNUSA
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7
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Ordon J, Kiel N, Becker D, Kretschmer C, Schulze-Lefert P, Stuttmann J. Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two. PLANT METHODS 2023; 19:30. [PMID: 36978193 PMCID: PMC10053088 DOI: 10.1186/s13007-023-01010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In plant genome editing, RNA-guided nucleases such as Cas9 from Streptococcus pyogenes (SpCas9) predominantly induce small insertions or deletions at target sites. This can be used for inactivation of protein-coding genes by frame shift mutations. However, in some cases, it may be advantageous to delete larger chromosomal segments. This is achieved by simultaneously inducing double strand breaks upstream and downstream of the segment to be deleted. Experimental approaches for the deletion of larger chromosomal segments have not been systematically evaluated. RESULTS We designed three pairs of guide RNAs for deletion of a ~ 2.2 kb chromosomal segment containing the Arabidopsis WRKY30 locus. We tested how the combination of guide RNA pairs and co-expression of the exonuclease TREX2 affect the frequency of wrky30 deletions in editing experiments. Our data demonstrate that compared to one pair of guide RNAs, two pairs increase the frequency of chromosomal deletions. The exonuclease TREX2 enhanced mutation frequency at individual target sites and shifted the mutation profile towards larger deletions. However, TREX2 did not elevate the frequency of chromosomal segment deletions. CONCLUSIONS Multiplex editing with at least two pairs of guide RNAs (four guide RNAs in total) elevates the frequency of chromosomal segment deletions at least at the AtWRKY30 locus, and thus simplifies the selection of corresponding mutants. Co-expression of the TREX2 exonuclease can be used as a general strategy to increase editing efficiency in Arabidopsis without obvious negative effects.
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Affiliation(s)
- Jana Ordon
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
| | - Niklas Kiel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dieter Becker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, D06120, Halle, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Johannes Stuttmann
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany.
- CEA, CNRS, BIAM, UMR7265, LEMiRE (Rhizosphère et Interactions sol-plante-microbiote), Aix Marseille University, 13115, Saint-Paul lez Durance, France.
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8
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Chamness JC, Kumar J, Cruz AJ, Rhuby E, Holum MJ, Cody JP, Tibebu R, Gamo ME, Starker CG, Zhang F, Voytas DF. An extensible vector toolkit and parts library for advanced engineering of plant genomes. THE PLANT GENOME 2023:e20312. [PMID: 36896468 DOI: 10.1002/tpg2.20312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T-DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site-specific recombinases. Finally, we use a series of dual-luciferase assays to measure contributions to expression from promoters, terminators, and from cross-cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
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Affiliation(s)
- James C Chamness
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jitesh Kumar
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Anna J Cruz
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Elissa Rhuby
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Mason J Holum
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Jon P Cody
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Redeat Tibebu
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Feng Zhang
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
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9
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Casas-Mollano JA, Zinselmeier M, Sychla A, Smanski MJ. Efficient gene activation in plants by the MoonTag programmable transcriptional activator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528671. [PMID: 36824723 PMCID: PMC9948947 DOI: 10.1101/2023.02.15.528671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
CRISPR/Cas-based transcriptional activators have been developed to induce gene expression in eukaryotic and prokaryotic organisms. The main advantages of CRISPR-Cas based systems is that they can achieve high levels of transcriptional activation and are very easy to program via pairing between the guide RNA and the DNA target strand. SunTag is a second-generation system that activates transcription by recruiting multiple copies of an activation domain (AD) to its target promoters. SunTag is a strong activator; however, in some species it is difficult to stably express. To overcome this problem, we designed MoonTag, a new activator that worked on the same basic principle as SunTag, but whose components are better tolerated when stably expressed in transgenic plants. We demonstrate that MoonTag is capable of inducing high levels of transcription in all plants tested. In Setaria, MoonTag is capable of inducing high levels of transcription of reporter genes as well as of endogenous genes. More important, MoonTag components are expressed in transgenic plants to high levels without any deleterious effects. MoonTag is also able to efficiently activate genes in eudicotyledonous species such as Arabidopsis and tomato. Finally, we show that MoonTag activation is functional across a range of temperatures, which is promising for potential field applications.
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10
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Sustek-Sánchez F, Rognli OA, Rostoks N, Sõmera M, Jaškūnė K, Kovi MR, Statkevičiūtė G, Sarmiento C. Improving abiotic stress tolerance of forage grasses - prospects of using genome editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1127532. [PMID: 36824201 PMCID: PMC9941169 DOI: 10.3389/fpls.2023.1127532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Due to an increase in the consumption of food, feed, and fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to obtain high-yielding crops that can adapt to future climate changes. Currently, the main feed source used for ruminant livestock production is forage grasses. In temperate climate zones, perennial grasses grown for feed are widely distributed and tend to suffer under unfavorable environmental conditions. Genome editing has been shown to be an effective tool for the development of abiotic stress-resistant plants. The highly versatile CRISPR-Cas system enables increasingly complex modifications in genomes while maintaining precision and low off-target frequency mutations. In this review, we provide an overview of forage grass species that have been subjected to genome editing. We offer a perspective view on the generation of plants resilient to abiotic stresses. Due to the broad factors contributing to these stresses the review focuses on drought, salt, heat, and cold stresses. The application of new genomic techniques (e.g., CRISPR-Cas) allows addressing several challenges caused by climate change and abiotic stresses for developing forage grass cultivars with improved adaptation to the future climatic conditions. Genome editing will contribute towards developing safe and sustainable food systems.
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Affiliation(s)
- Ferenz Sustek-Sánchez
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Odd Arne Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Nils Rostoks
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Latvia, Riga, Latvia
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Mallikarjuna Rao Kovi
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gražina Statkevičiūtė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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11
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Li H, Li L, Wu W, Wang F, Zhou F, Lin Y. SvSTL1 in the large subunit family of ribonucleotide reductases plays a major role in chloroplast development of Setaria viridis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:625-641. [PMID: 35608125 DOI: 10.1111/tpj.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes in DNA synthesis. However, little is known about the RNRs in plants. Here, we identified a svstl1 mutant from the self-created ethyl methanesulfonate (EMS) mutant library of Setaria viridis. The mutant leaves exhibited a bleaching phenotype at the heading stage. Paraffin section analysis showed the destruction of the C4 Kranz anatomy. Transmission electron microscopy results further demonstrated the severely disturbed development of some chloroplasts. MutMap analysis revealed that the SvSTL1 gene is the primary candidate, encoding a large subunit of RNRs. Complementation experiments confirmed that SvSTL1 is responsible for the phenotype of svstl1. There are two additional RNR large subunit homologs in S. viridis, SvSTL2 and SvSTL3. To further understand the functions of these three RNR large subunit genes, a series of mutants were generated via CRISPR/Cas9 technology. In striking contrast to the finding that all three SvSTLs interact with the RNR small subunit, the phenotype varied along with the copies of chloroplast genome among different svstl single mutants: the svstl1 mutant exhibited pronounced chloroplast development and significantly fewer copies of the chloroplast genome than the svstl2 or svstl3 single mutants. These results suggested that SvSTL1 plays a major role in the optimal function of RNRs and is essential for chloroplast development. Furthermore, through the analysis of double and triple mutants, the study provides new insights into the finely tuned coordination among SvSTLs to maintain normal chloroplast development in the emerging C4 model plant S. viridis.
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Affiliation(s)
- Huanying Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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12
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:cells11142157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Correspondence:
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13
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Read A, Weiss T, Crisp PA, Liang Z, Noshay J, Menard CC, Wang C, Song M, Hirsch CN, Springer NM, Zhang F. Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:103-116. [PMID: 35436373 PMCID: PMC9541237 DOI: 10.1111/tpj.15781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 05/17/2023]
Abstract
The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole-genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for the locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild-type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.
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Affiliation(s)
- Andrew Read
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Trevor Weiss
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Peter A. Crisp
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
| | - Zhikai Liang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Jaclyn Noshay
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Claire C. Menard
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Chunfang Wang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Meredith Song
- Department of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisMinnesota55108USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Nathan M. Springer
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Feng Zhang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
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14
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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15
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Laforest LC, Nadakuduti SS. Advances in Delivery Mechanisms of CRISPR Gene-Editing Reagents in Plants. Front Genome Ed 2022; 4:830178. [PMID: 35141701 PMCID: PMC8819002 DOI: 10.3389/fgeed.2022.830178] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/05/2022] [Indexed: 01/18/2023] Open
Abstract
Gene-editing by CRISPR/Cas systems has revolutionized plant biology by serving as a functional genomics tool. It has tremendously advanced plant breeding and crop improvement by accelerating the development of improved cultivars, creating genetic variability, and aiding in domestication of wild and orphan crops. Gene-editing is a rapidly evolving field. Several advancements include development of different Cas effectors with increased target range, efficacy, and enhanced capacity for precise DNA modifications with base editing and prime editing. The existing toolbox of various CRISPR reagents facilitate gene knockouts, targeted gene insertions, precise base substitutions, and multiplexing. However, the major challenge in plant genome-editing remains the efficient delivery of these reagents into plant cells. Plants have larger and more complex genome structures compared to other living systems due to the common occurrence of polyploidy and other genome re-arrangements. Further, rigid cell walls surrounding plant cells deter the entry of any foreign biomolecules. Unfortunately, genetic transformation to deliver gene-editing reagents has been established only in a limited number of plant species. Recently, there has been significant progress in CRISPR reagents delivery in plants. This review focuses on exploring these delivery mechanisms categorized into Agrobacterium-mediated delivery and breakthroughs, particle bombardment-based delivery of biomolecules and recent improvements, and protoplasts, a versatile system for gene-editing and regeneration in plants. The ultimate goal in plant gene-editing is to establish highly efficient and genotype-independent reagent delivery mechanisms for editing multiple targets simultaneously and achieve DNA-free gene-edited plants at scale.
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Affiliation(s)
- Larissa C. Laforest
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Satya Swathi Nadakuduti
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, United States
- *Correspondence: Satya Swathi Nadakuduti,
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16
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Banakar R, Schubert M, Kurgan G, Rai KM, Beaudoin SF, Collingwood MA, Vakulskas CA, Wang K, Zhang F. Efficiency, Specificity and Temperature Sensitivity of Cas9 and Cas12a RNPs for DNA-free Genome Editing in Plants. Front Genome Ed 2022; 3:760820. [PMID: 35098208 PMCID: PMC8790294 DOI: 10.3389/fgeed.2021.760820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Delivery of genome editing reagents using CRISPR-Cas ribonucleoproteins (RNPs) transfection offers several advantages over plasmid DNA-based delivery methods, including reduced off-target editing effects, mitigation of random integration of non-native DNA fragments, independence of vector constructions, and less regulatory restrictions. Compared to the use in animal systems, RNP-mediated genome editing is still at the early development stage in plants. In this study, we established an efficient and simplified protoplast-based genome editing platform for CRISPR-Cas RNP delivery, and then evaluated the efficiency, specificity, and temperature sensitivity of six Cas9 and Cas12a proteins. Our results demonstrated that Cas9 and Cas12a RNP delivery resulted in genome editing frequencies (8.7-41.2%) at various temperature conditions, 22°C, 26°C, and 37°C, with no significant temperature sensitivity. LbCas12a often exhibited the highest activities, while AsCas12a demonstrated higher sequence specificity. The high activities of CRISPR-Cas RNPs at 22° and 26°C, the temperature preferred by plant transformation and tissue culture, led to high mutagenesis efficiencies (34.0-85.2%) in the protoplast-regenerated calli and plants with the heritable mutants recovered in the next generation. This RNP delivery approach was further extended to pennycress (Thlaspi arvense), soybean (Glycine max) and Setaria viridis with up to 70.2% mutagenesis frequency. Together, this study sheds light on the choice of RNP reagents to achieve efficient transgene-free genome editing in plants.
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Affiliation(s)
- Raviraj Banakar
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | | | - Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA, United States
| | - Krishan Mohan Rai
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | | | | | | | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
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17
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Huang X, Wang Y, Wang N. Highly Efficient Generation of Canker-Resistant Sweet Orange Enabled by an Improved CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2022; 12:769907. [PMID: 35087548 PMCID: PMC8787272 DOI: 10.3389/fpls.2021.769907] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/09/2021] [Indexed: 06/02/2023]
Abstract
Sweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes, and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously [dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, citrus U6 (CsU6) to drive sgRNA expression], we further improved our CRISPR/Cas9 system by choosing superior promoters [Cestrum yellow leaf curling virus (CmYLCV) or Citrus sinensis ubiquitin (CsUbi) promoter] to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker-resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease-resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.
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18
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Banakar R, Rai KM, Zhang F. CRISPR DNA- and RNP-Mediated Genome Editing via Nicotiana benthamiana Protoplast Transformation and Regeneration. Methods Mol Biol 2022; 2464:65-82. [PMID: 35258825 DOI: 10.1007/978-1-0716-2164-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated system) has become the multipurpose tool to manipulate plant genome via their programmable sequence recognition, binding, and cleavage activities. Efficient plant genome modification often requires robust plant transformation. For most plant species, the CRISPR/Cas reagents are delivered into plants as plasmids by Agrobacterium-mediated T-DNA transfer or biolistic approaches. However, these methods are generally inefficient, heavily genotype dependent, and low throughput. Among the alternative plant transformation approaches, the protoplast-based transformation holds the potential to directly deliver DNA, RNA, or protein molecules into plant cells in an efficient and high-throughput manner. Here, we presented a robust and simplified protocol for protoplast-based DNA/ribonucleoprotein (RNP )-mediated genome editing in the model species Nicotiana benthamiana. Using this protocol, we have achieved the gene editing efficiency at 30-60% in protoplasts and 50-80% in regenerated calli and plants. The edited protoplasts can be readily regenerated without selection agents owing to highly efficient DNA or preassembled RNP transformation frequency. Lastly, this protocol utilized an improved culture media regime to overcome the complex media composition used in the previous studies. It offers quick turnaround time and higher throughput to facilitate the development of new genetic engineering technologies and holds the promise to combine with other genetic and genomic tools for fundamental and translational plant research.
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Affiliation(s)
- Raviraj Banakar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
| | - Krishan M Rai
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA.
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19
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Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Mol Cell 2021; 82:333-347. [PMID: 34968414 DOI: 10.1016/j.molcel.2021.12.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023]
Abstract
The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.
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Affiliation(s)
- Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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20
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Venezia M, Creasey Krainer KM. Current Advancements and Limitations of Gene Editing in Orphan Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:742932. [PMID: 34630494 PMCID: PMC8493294 DOI: 10.3389/fpls.2021.742932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 05/23/2023]
Abstract
Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.
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21
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Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:35-54. [PMID: 34435370 DOI: 10.1111/nyas.14675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
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Affiliation(s)
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, and the Joint BioEnergy Institute, Davis, California
| | - Daniel Voytas
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Feng Zhang
- College of Biological Sciences, University of Minnesota, St. Paul, Minnesota
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ayumu Takatsuka
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Steven E Jacobsen
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Department of Molecular, Cell and Developmental Biology; and Howard Hughes Medical Institute, University of California, Los Angeles, California
| | - Seiichi Toki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, and College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York, and Plant Breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Trevor Weiss
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, Iowa
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina
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22
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Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int J Mol Sci 2021; 22:8093. [PMID: 34360856 PMCID: PMC8348985 DOI: 10.3390/ijms22158093] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Thattantavide Anju
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sushil Kumar
- Department of Botany, Govt. Degree College, Kishtwar 182204, Jammu and Kashmir, India;
| | - Sushil Satish Chhapekar
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Sajana Sreedharan
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sonam Singh
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Su Ryun Choi
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Yong Pyo Lim
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
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Michalski K, Hertig C, Mańkowski DR, Kumlehn J, Zimny J, Linkiewicz AM. Functional Validation of cas9/guideRNA Constructs for Site-Directed Mutagenesis of Triticale ABA8'OH1 loci. Int J Mol Sci 2021; 22:7038. [PMID: 34210100 PMCID: PMC8269138 DOI: 10.3390/ijms22137038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/02/2022] Open
Abstract
Cas endonuclease-mediated genome editing provides a long-awaited molecular biological approach to the modification of predefined genomic target sequences in living organisms. Although cas9/guide (g)RNA constructs are straightforward to assemble and can be customized to target virtually any site in the plant genome, the implementation of this technology can be cumbersome, especially in species like triticale that are difficult to transform, for which only limited genome information is available and/or which carry comparatively large genomes. To cope with these challenges, we have pre-validated cas9/gRNA constructs (1) by frameshift restitution of a reporter gene co-introduced by ballistic DNA transfer to barley epidermis cells, and (2) via transfection in triticale protoplasts followed by either a T7E1-based cleavage assay or by deep-sequencing of target-specific PCR amplicons. For exemplification, we addressed the triticale ABA 8'-hydroxylase 1 gene, one of the putative determinants of pre-harvest sprouting of grains. We further show that in-del induction frequency in triticalecan beincreased by TREX2 nuclease activity, which holds true for both well- and poorly performing gRNAs. The presented results constitute a sound basis for the targeted induction of heritable modifications in triticale genes.
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Affiliation(s)
- Krzysztof Michalski
- GMO Controlling Laboratory, Plant Biotechnology and Cytogenetics Department, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.M.); (J.Z.)
| | - Christian Hertig
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany; (J.K.); (C.H.)
| | - Dariusz R. Mańkowski
- Laboratory of Seed Production and Plant Breeding Economics, Department of Seed Science and Technology, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland;
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany; (J.K.); (C.H.)
| | - Janusz Zimny
- GMO Controlling Laboratory, Plant Biotechnology and Cytogenetics Department, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.M.); (J.Z.)
| | - Anna M. Linkiewicz
- GMO Controlling Laboratory, Plant Biotechnology and Cytogenetics Department, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.M.); (J.Z.)
- Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3 Street, 01-938 Warsaw, Poland
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24
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Basso MF, Duarte KE, Santiago TR, de Souza WR, Garcia BDO, da Cunha BDB, Kobayashi AK, Molinari HBC. Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:227-238. [PMID: 34393601 PMCID: PMC8329270 DOI: 10.5511/plantbiotechnology.21.0407a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/07/2021] [Indexed: 05/05/2023]
Abstract
The CRISPR/Cas9 system has been used for genome editing in several organisms, including higher plants. This system induces site-specific mutations in the genome based on the nucleotide sequence of engineered guide RNAs. The complex genomes of C4 grasses makes genome editing a challenge in key grass crops like maize (Zea mays), sorghum (Sorghum bicolor), Brachiaria spp., switchgrass (Panicum virgatum), and sugarcane (Saccharum spp.). Setaria viridis is a diploid C4 grass widely used as a model for these C4 crop plants. Here, an optimized CRISPR/Cas9 binary vector that exploits the non-homologous end joining (NHEJ) system was used to knockout a green fluorescent protein (gfp) transgene in S. viridis accession A10.1. Transformation of embryogenic callus by A. tumefaciens generated ten glufosinate-ammonium resistant transgenic events. In the T0 generation, 60% of the events were biallelic mutants in the gfp transgene with no detectable accumulation of GFP protein and without insertions or deletions in predicted off-target sites. The gfp mutations generated by CRISPR/Cas9 were stable and displayed Mendelian segregation in the T1 generation. Altogether, the system described here is a highly efficient genome editing system for S. viridis, an important model plant for functional genomics studies in C4 grasses. Also, this system is a potential tool for improvement of agronomic traits in C4 crop plants with complex genomes.
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Affiliation(s)
- Marcos Fernando Basso
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT, 78740-970, Brazil
| | - Karoline Estefani Duarte
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Thais Ribeiro Santiago
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- Departament of Phytopathology, Federal University of Brasília, Brasília (UNB), Distrito Federal, 70910-900, Brazil
| | - Wagner Rodrigo de Souza
- Center for Natural and Human Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, São Paulo, 09606-045, Brazil
| | - Bruno de Oliveira Garcia
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Bárbara Dias Brito da Cunha
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Adilson Kenji Kobayashi
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
| | - Hugo Bruno Correa Molinari
- National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, DF, 70770-901, Brazil
- E-mail: Tel: +55-61-3448-2307, Fax: +55-61-34481598
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25
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Stuttmann J, Barthel K, Martin P, Ordon J, Erickson JL, Herr R, Ferik F, Kretschmer C, Berner T, Keilwagen J, Marillonnet S, Bonas U. Highly efficient multiplex editing: one-shot generation of 8× Nicotiana benthamiana and 12× Arabidopsis mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:8-22. [PMID: 33577114 DOI: 10.1111/tpj.15197] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Genome editing by RNA-guided nucleases, such as SpCas9, has been used in numerous different plant species. However, to what extent multiple independent loci can be targeted simultaneously by multiplexing has not been well documented. Here, we developed a toolkit, based on a highly intron-optimized zCas9i gene, which allows assembly of nuclease constructs expressing up to 32 single guide RNAs (sgRNAs). We used this toolkit to explore the limits of multiplexing in two major model species, and report on the isolation of transgene-free octuple (8×) Nicotiana benthamiana and duodecuple (12×) Arabidopsis thaliana mutant lines in a single generation (T1 and T2 , respectively). We developed novel counter-selection markers for N. benthamiana, most importantly Sl-FAST2, comparable to the well-established Arabidopsis seed fluorescence marker, and FCY-UPP, based on the production of toxic 5-fluorouracil in the presence of a precursor. Targeting eight genes with an array of nine different sgRNAs and relying on FCY-UPP for selection of non-transgenic T1 , we identified N. benthamiana mutant lines with astonishingly high efficiencies: All analyzed plants carried mutations in all genes (approximately 112/116 target sites edited). Furthermore, we targeted 12 genes by an array of 24 sgRNAs in A. thaliana. Efficiency was significantly lower in A. thaliana, and our results indicate Cas9 availability is the limiting factor in such higher-order multiplexing applications. We identified a duodecuple mutant line by a combination of phenotypic screening and amplicon sequencing. The resources and results presented provide new perspectives for how multiplexing can be used to generate complex genotypes or to functionally interrogate groups of candidate genes.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Karen Barthel
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Patrick Martin
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jana Ordon
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jessica L Erickson
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Rosalie Herr
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Filiz Ferik
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Carola Kretschmer
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Ulla Bonas
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
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26
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Peng R, Zhang B. Foxtail Millet: A New Model for C4 Plants. TRENDS IN PLANT SCIENCE 2021; 26:199-201. [PMID: 33358112 DOI: 10.1016/j.tplants.2020.12.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 05/29/2023]
Abstract
Arabidopsis and rice are major models for C3 plants, but we still lack a model for C4 plants. Recently, Yang and coworkers developed foxtail millet as a C4 plant model; with the rapid development of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas technology, this will open a new era for plant functional studies and crop improvement.
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Affiliation(s)
- Renhai Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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27
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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28
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Ye CY, Fan L. Orphan Crops and their Wild Relatives in the Genomic Era. MOLECULAR PLANT 2021; 14:27-39. [PMID: 33346062 DOI: 10.1016/j.molp.2020.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 05/06/2023]
Abstract
More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572024, China.
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29
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Thielen PM, Pendleton AL, Player RA, Bowden KV, Lawton TJ, Wisecaver JH. Reference Genome for the Highly Transformable Setaria viridis ME034V. G3 (BETHESDA, MD.) 2020; 10:3467-3478. [PMID: 32694197 PMCID: PMC7534418 DOI: 10.1534/g3.120.401345] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.
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Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Player
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Kenneth V Bowden
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Thomas J Lawton
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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