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Vu TV, Doan DTH, Tran MT, Sung YW, Song YJ, Kim JY. Improvement of the LbCas12a-crRNA System for Efficient Gene Targeting in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:722552. [PMID: 34447405 PMCID: PMC8383147 DOI: 10.3389/fpls.2021.722552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/16/2021] [Indexed: 05/03/2023]
Abstract
Plant gene targeting (GT) can be utilized to precisely replace up to several kilobases of a plant genome. Recent studies using the powerful clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nucleases significantly improved plant GT efficiency. However, GT for loci without associated selection markers is still inefficient. We previously utilized Lachnospiraceae bacterium Cas12a (LbCas12a) in combination with a replicon for tomato GT and obtained high GT efficiency with some selection markers. In this study, we advance our GT system by inhibiting the cNHEJ pathway with small chemical molecules such as NU7441. Further optimization of the GT is also possible with the treatment of silver nitrate possibly via its pronounced actions in ethylene inhibition and polyamine production. Importantly, the GT efficiency is significantly enhanced with the use of a temperature-tolerant LbCas12a (ttLbCas12a) that is capable of performing target cleavage even at low temperatures. Targeted deep sequencing, as well as conventional methods, are used for the assessment of the editing efficiency at both cell and plant levels. Our work demonstrates the significance of the selection of gene scissors, the appropriate design and number of LbCas12a crRNAs, the use of chemical treatments, and the establishment of favorable experimental conditions for further enhancement of plant HDR to enable efficient GT in tomato.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Hanoi, Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Crop Science and Rural Development Division, College of Agriculture, Bac Lieu University, Bạc Liêu, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Life Science, Gyeongsang National University, Jinju, South Korea
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Chumakov MI. Protein apparatus for horizontal transfer of agrobacterial T-DNA to eukaryotic cells. BIOCHEMISTRY (MOSCOW) 2013; 78:1321-32. [DOI: 10.1134/s000629791312002x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lusser M, Davies HV. Comparative regulatory approaches for groups of new plant breeding techniques. N Biotechnol 2013; 30:437-46. [PMID: 23474021 DOI: 10.1016/j.nbt.2013.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/31/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
This manuscript provides insights into ongoing debates on the regulatory issues surrounding groups of biotechnology-driven 'New Plant Breeding Techniques' (NPBTs). It presents the outcomes of preliminary discussions and in some cases the initial decisions taken by regulators in the following countries: Argentina, Australia, Canada, EU, Japan, South Africa and USA. In the light of these discussions we suggest in this manuscript a structured approach to make the evaluation more consistent and efficient. The issue appears to be complex as these groups of new technologies vary widely in both the technologies deployed and their impact on heritable changes in the plant genome. An added complication is that the legislation, definitions and regulatory approaches for biotechnology-derived crops differ significantly between these countries. There are therefore concerns that this situation will lead to non-harmonised regulatory approaches and asynchronous development and marketing of such crops resulting in trade disruptions.
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Affiliation(s)
- Maria Lusser
- European Commission, Institute of Prospective Technological Studies (IPTS), Joint Research Center (JRC), Ed. Expo, c/Inca Garcilaso 3, E-41092 Sevilla, Spain.
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Da Ines O, White CI. Gene Site-Specific Insertion in Plants. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Tzfira T, Weinthal D, Marton I, Zeevi V, Zuker A, Vainstein A. Genome modifications in plant cells by custom-made restriction enzymes. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:373-89. [PMID: 22469004 DOI: 10.1111/j.1467-7652.2011.00672.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genome editing, i.e. the ability to mutagenize, insert, delete and replace sequences, in living cells is a powerful and highly desirable method that could potentially revolutionize plant basic research and applied biotechnology. Indeed, various research groups from academia and industry are in a race to devise methods and develop tools that will enable not only site-specific mutagenesis but also controlled foreign DNA integration and replacement of native and transgene sequences by foreign DNA, in living plant cells. In recent years, much of the progress seen in gene targeting in plant cells has been attributed to the development of zinc finger nucleases and other novel restriction enzymes for use as molecular DNA scissors. The induction of double-strand breaks at specific genomic locations by zinc finger nucleases and other novel restriction enzymes results in a wide variety of genetic changes, which range from gene addition to the replacement, deletion and site-specific mutagenesis of endogenous and heterologous genes in living plant cells. In this review, we discuss the principles and tools for restriction enzyme-mediated gene targeting in plant cells, as well as their current and prospective use for gene targeting in model and crop plants.
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Affiliation(s)
- Tzvi Tzfira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, Snoek LB, Millenaar FF, Schulkes RK, van Driel R, Voesenek LACJ, Spillane C, Pikaard CS, Fransz P, Peeters AJM. Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet 2009; 5:e1000638. [PMID: 19730687 PMCID: PMC2728481 DOI: 10.1371/journal.pgen.1000638] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 08/08/2009] [Indexed: 11/18/2022] Open
Abstract
Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process. The habitat of the plant model species Arabidopsis thaliana can be found throughout the Northern hemisphere. As a consequence, individual populations have acclimated to a great diversity of environmental conditions. This is reflected by a wealth of natural genetic variation in many phenotypic traits. We utilized this natural variation via a novel approach, combining microscopic examination, quantitative genetics, and analysis of environmental parameters, to understand the regulation of nuclear chromatin compaction in leaf mesophyll cells. We show that the level of chromatin compaction among natural Arabidopsis thaliana accessions correlates with latitude of origin and depends on local light intensity. Our study provides evidence that the photoreceptor PHYTOCHROME-B (PHYB) and the histone modifier HISTONE DEACETYLASE 6 (HDA6) are positive regulators of global chromatin organization in a light-dependent manner. In addition, HDA6 specifically controls light-mediated chromatin compaction of the Nucleolar Organizing Regions (NORs). We propose that the observed light-controlled plasticity of chromatin plays a role in acclimation and survival of plants in their natural environment.
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Affiliation(s)
- Federico Tessadori
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Penka Pavlova
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory of Genetics, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Rachel Clifton
- Genetics & Biotechnology Laboratory, Department of Biochemistry & Biosciences Institute, University College Cork, Cork, Republic of Ireland
| | - Frédéric Pontvianne
- Biology Department, Washington University, St. Louis, Missouri, United States of America
| | - L. Basten Snoek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Frank F. Millenaar
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Roeland Kees Schulkes
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Roel van Driel
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Charles Spillane
- Genetics & Biotechnology Laboratory, Department of Biochemistry & Biosciences Institute, University College Cork, Cork, Republic of Ireland
| | - Craig S. Pikaard
- Biology Department, Washington University, St. Louis, Missouri, United States of America
| | - Paul Fransz
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (PF); (AJMP)
| | - Anton J. M. Peeters
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail: (PF); (AJMP)
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Vasil IK. Molecular genetic improvement of cereals: transgenic wheat (Triticum aestivum L.). PLANT CELL REPORTS 2007; 26:1133-54. [PMID: 17431631 DOI: 10.1007/s00299-007-0338-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 05/14/2023]
Abstract
Only modest progress has been made in the molecular genetic improvement of wheat following the production of the first transgenic plants in 1992, made possible by the development of efficient, long-term regenerable embryogenic cultures derived from immature embryos and use of the biolistics method for the direct delivery of DNA into regenerable cells. Transgenic lines expressing genes that confer resistance to environmentally friendly non-selective herbicides, and pests and pathogens have been produced, in addition to lines with improved bread-making and nutritional qualities; some of these are ready for commercial production. Reduction of losses caused by weeds, pests and pathogens in such plants not only indirectly increases available arable land and fresh water supplies, but also conserves energy and natural resources. Nevertheless, the work carried out thus far can be considered only the beginning, as many difficult tasks lie ahead and much remains to be done. The challenge now is to produce higher-yielding varieties that are more nutritious, and are resistant or tolerant to a wide variety of biotic as well as abiotic stresses (especially drought, salinity, heavy metal toxicity) that currently cause substantial losses in productivity. How well we will meet this challenge for wheat, and indeed for other cereal and non-cereal crops, will depend largely on establishing collaborative partnerships between breeders, molecular biologists, biotechnologists and industry, and on how effectively they make use of the knowledge and insights gained from basic studies in plant biology and genetics, the sequencing of plant/cereal genomes, the discovery of synteny in cereals, and the availability of DNA-based markers and increasingly detailed chromosomal maps.
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Affiliation(s)
- Indra K Vasil
- University of Florida, Gainesville, FL 32611-0690, USA.
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Mitchell-Olds T, Schmitt J. Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 2006; 441:947-52. [PMID: 16791187 DOI: 10.1038/nature04878] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.
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Affiliation(s)
- Thomas Mitchell-Olds
- Department of Biology, PO Box 91000, Duke University, Durham, North Carolina 27708, USA.
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Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba, Japan
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