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Campa M, Miranda S, Licciardello C, Lashbrooke JG, Dalla Costa L, Guan Q, Spök A, Malnoy M. Application of new breeding techniques in fruit trees. PLANT PHYSIOLOGY 2024; 194:1304-1322. [PMID: 37394947 DOI: 10.1093/plphys/kiad374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
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Affiliation(s)
- Manuela Campa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Simón Miranda
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | | | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Mickael Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
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Švara A, De Storme N, Carpentier S, Keulemans W, De Coninck B. Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab ( Venturia inaequalis) in apple cultivars ( Malus × domestica). HORTICULTURE RESEARCH 2024; 11:uhae002. [PMID: 38371632 PMCID: PMC10873587 DOI: 10.1093/hr/uhae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024]
Abstract
Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
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Affiliation(s)
- Anže Švara
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Genetic resources, Bioversity International, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Barbara De Coninck
- Laboratory of Plant Health and Protection, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
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Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
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Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
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Hoengenaert L, Van Doorsselaere J, Vanholme R, Boerjan W. Microparticle-mediated CRISPR DNA delivery for genome editing in poplar. FRONTIERS IN PLANT SCIENCE 2023; 14:1286663. [PMID: 38023888 PMCID: PMC10679337 DOI: 10.3389/fpls.2023.1286663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The use of CRISPR/Cas9 is currently the method of choice for precise genome engineering in plants, including in the biomass crop poplar. The most commonly used method for delivering CRISPR/Cas9 and its components in poplar is via Agrobacterium-mediated transformation, that besides the desired gene-editing event also results in stable T-DNA integration. Here we explore the delivery of the gene-editing reagents via DNA-coated microparticle bombardment into the model tree Populus tremula x P. alba to evaluate its potential for developing transgene-free, gene-edited trees, as well as its potential for integrating donor DNA at specific target sites. Using an optimized transformation method, which favors the regeneration of plants that transiently express the genes on the delivered donor DNA, we regenerated gene-edited plants that are free of the Cas9 and the antibiotic resistance-encoding transgenes. In addition, we report the frequent integration of donor DNA fragments at the Cas9-induced double-strand break, opening opportunities toward targeted gene insertions.
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Affiliation(s)
- Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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Jacobson S, Bondarchuk N, Nguyen TA, Canada A, McCord L, Artlip TS, Welser P, Klocko AL. Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple. PLANTS (BASEL, SWITZERLAND) 2023; 12:3693. [PMID: 37960050 PMCID: PMC10649517 DOI: 10.3390/plants12213693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.
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Affiliation(s)
- Seth Jacobson
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Natalie Bondarchuk
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Thy Anh Nguyen
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Allison Canada
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Logan McCord
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Timothy S. Artlip
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Philipp Welser
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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6
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Huang X, Jia H, Xu J, Wang Y, Wen J, Wang N. Transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation via a co-editing strategy. NATURE PLANTS 2023; 9:1591-1597. [PMID: 37723203 DOI: 10.1038/s41477-023-01520-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Transgene-free plant genome editing in the T0 generation is highly desirable but challenging1,2. Here we achieved such a goal using a co-editing strategy via Agrobacterium-mediated transient expression of cytosine base editor to edit ALS encoding acetolactate synthase to confer herbicide chlorsulfuron resistance as a selection marker, Cas12a/CRISPR RNA for editing gene(s) of interest, and green fluorescent protein for selecting transgene-free transformants. The biallelic/homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 1.9% to 42.1% in tomato, tobacco, potato and citrus. This co-editing strategy is particularly useful for transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation.
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Affiliation(s)
- Xiaoen Huang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jiawen Wen
- Citrus Research and Education Center, Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
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Sardar A. Genetic amelioration of fruit and vegetable crops to increase biotic and abiotic stress resistance through CRISPR Genome Editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1260102. [PMID: 37841604 PMCID: PMC10570431 DOI: 10.3389/fpls.2023.1260102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Environmental changes and increasing population are major concerns for crop production and food security as a whole. To address this, researchers had focussed on the improvement of cereals and pulses and have made considerable progress till the beginning of this decade. However, cereals and pulses together, without vegetables and fruits, are inadequate to meet the dietary and nutritional demands of human life. Production of good quality vegetables and fruits is highly challenging owing to their perishable nature and short shelf life as well as abiotic and biotic stresses encountered during pre- and post-harvest. Genetic engineering approaches to produce good quality, to increase shelf life and stress-resistance, and to change the time of flowering and fruit ripening by introducing foreign genes to produce genetically modified crops were quite successful. However, several biosafety concerns, such as the risk of transgene-outcrossing, limited their production, marketing, and consumption. Modern genome editing techniques, like the CRISPR/Cas9 system, provide a perfect solution in this scenario, as it can produce transgene-free genetically edited plants. Hence, these genetically edited plants can easily satisfy the biosafety norms for crop production and consumption. This review highlights the potential of the CRISPR/Cas9 system for the successful generation of abiotic and biotic stress resistance and thereby improving the quality, yield, and overall productivity of vegetables and fruits.
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Affiliation(s)
- Atish Sardar
- Department of Botany, Jogesh Chandra Chaudhuri College, West Bengal, Kolkata, India
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Dougherty L, Borejsza-Wysocka E, Miaule A, Wang P, Zheng D, Jansen M, Brown S, Piñeros M, Dardick C, Xu K. A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus. PLANT PHYSIOLOGY 2023; 193:1142-1160. [PMID: 37394917 DOI: 10.1093/plphys/kiad373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Ewa Borejsza-Wysocka
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Alexandre Miaule
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
| | - Ping Wang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Desen Zheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Michael Jansen
- United States Department of Agriculture-Agricultural Research Service, Systematic Entomology Laboratory, Electron and Confocal Microscopy Unit, Beltsville, MD 20705, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Miguel Piñeros
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Christopher Dardick
- United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
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Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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11
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Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding. Curr Issues Mol Biol 2023; 45:918-935. [PMID: 36826004 PMCID: PMC9955079 DOI: 10.3390/cimb45020059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.
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Nerva L, Dalla Costa L, Ciacciulli A, Sabbadini S, Pavese V, Dondini L, Vendramin E, Caboni E, Perrone I, Moglia A, Zenoni S, Michelotti V, Micali S, La Malfa S, Gentile A, Tartarini S, Mezzetti B, Botta R, Verde I, Velasco R, Malnoy MA, Licciardello C. The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives. Int J Mol Sci 2023; 24:ijms24020977. [PMID: 36674493 PMCID: PMC9861864 DOI: 10.3390/ijms24020977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023] Open
Abstract
Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.
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Affiliation(s)
- Luca Nerva
- Research Center for Viticulture and Enology, Council for Agricultural Research and Economics, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all’Adige, Italy
| | - Angelo Ciacciulli
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Vera Pavese
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Luca Dondini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elisa Vendramin
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Emilia Caboni
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Vania Michelotti
- Research Center for Genomics and Bioinformatics, Council for Agricultural Research and Economics, 29017 Fiorenzuola D’Arda, Italy
| | - Sabrina Micali
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Stefano La Malfa
- Department of Biotechnology, University of Catania, 95124 Catania, Italy
| | - Alessandra Gentile
- Department of Biotechnology, University of Catania, 95124 Catania, Italy
| | - Stefano Tartarini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Bruno Mezzetti
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Roberto Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Ignazio Verde
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Riccardo Velasco
- Research Center for Viticulture and Enology, Council for Agricultural Research and Economics, 31015 Conegliano, Italy
| | - Mickael Arnaud Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all’Adige, Italy
- Correspondence: (M.A.M.); (C.L.); Tel.: +39-04-6161-5536 (M.A.M.); +39-09-5765-3104 (C.L.)
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
- Correspondence: (M.A.M.); (C.L.); Tel.: +39-04-6161-5536 (M.A.M.); +39-09-5765-3104 (C.L.)
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Vaia G, Pavese V, Moglia A, Cristofori V, Silvestri C. Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry. FRONTIERS IN PLANT SCIENCE 2022; 13:1074541. [PMID: 36589127 PMCID: PMC9800005 DOI: 10.3389/fpls.2022.1074541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Among the New Plant Breeding Techniques (NPBTs), the CRISPR/Cas9 system represents a useful tool for target gene editing, improving the traits of the plants rapidly. This technology allows targeting one or more sequences simultaneously, as well as introducing new genetic variations by homology-directed recombination. However, the technology of CRISPR/Cas9 remains a challenge for some polyploid woody species, since all the different alleles for which the mutation is required must be simultaneously targeted. In this work we describe improved protocols adapting the CRISPR/Cas9 system to highbush blueberry (Vaccinium corymbosum L.), using Agrobacterium-mediated transformation. As a proof of concept, we targeted the gene encoding for phytoene desaturase, whose mutation disrupts chlorophyll biosynthesis allowing for the visual assessment of knockout efficiency. Leaf explants of in vitro-cultured blueberry cv. Berkeley has been transformed with a CRISPR/Cas9 construct containing two guide RNAs (gRNA1 and gRNA2) targeting two conserved gene regions of pds and subsequently maintained on a selection medium enriched with kanamycin. After 4 weeks in culture on the selection medium, the kanamycin-resistant lines were isolated, and the genotyping of these lines through Sanger sequencing revealed successful gene editing. Some of mutant shoot lines included albino phenotypes, even if the editing efficiencies were quite low for both gRNAs, ranging between 2.1 and 9.6% for gRNA1 and 3.0 and 23.8 for gRNA2. Here we showed a very effective adventitious shoot regeneration protocol for the commercial cultivar of highbush blueberry "Berkeley", and a further improvement in the use of CRISPR/Cas9 system in Vaccinium corymbosum L., opening the way to the breeding mediated by biotechnological approaches.
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Affiliation(s)
- Giuseppe Vaia
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Valerio Cristofori
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Cristian Silvestri
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
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In Vitro Polyploid Induction of Highbush Blueberry through De Novo Shoot Organogenesis. PLANTS 2022; 11:plants11182349. [PMID: 36145750 PMCID: PMC9504489 DOI: 10.3390/plants11182349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022]
Abstract
Polyploid induction is of utmost importance in horticultural plants for the development of new varieties with desirable morphological and physiological traits. Polyploidy may occur naturally due to the formation of unreduced gametes or can be artificially induced by doubling the number of chromosomes in somatic cells. In this experiment, a protocol for in vitro polyploid induction of highbush blueberry (Vaccinium corymbosum L.) leaf tissues was studied by using different concentrations of colchicine and oryzalin. Oryzalin was found to be highly toxic to this species, while the adventitious shoot organogenesis media enriched with 25 and 250 µM colchicine was able to induce polyploidization, with significant differences among the treatments used. Higher concentrations of both antimitotic agents led to the browning and death of the leaf tissues. The polyploids obtained showed several morphological differences when compared with the diploid shoots. Flow cytometry analysis was used to confirm the ploidy level of the regenerated shoots, demonstrating that a total of 15 tetraploids and 34 mixoploids were obtained. The stomatal sizes (length and width) of the tetraploids were larger than those of the diploids, but a reduced stomatal density was observed as compared to the controls. These shoots will be acclimatized and grown until they reach the reproductive phase in order to test their potential appeal as new varieties or their use for breeding and genetic improvement.
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15
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CRISPR-Based Genome Editing and Its Applications in Woody Plants. Int J Mol Sci 2022; 23:ijms231710175. [PMID: 36077571 PMCID: PMC9456532 DOI: 10.3390/ijms231710175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/31/2022] [Indexed: 12/21/2022] Open
Abstract
CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants.
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Dhakate P, Sehgal D, Vaishnavi S, Chandra A, Singh A, Raina SN, Rajpal VR. Comprehending the evolution of gene editing platforms for crop trait improvement. Front Genet 2022; 13:876987. [PMID: 36082000 PMCID: PMC9445674 DOI: 10.3389/fgene.2022.876987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), to address the problem of associated off-targets. The adaptation of this platform led to the development of concepts such as epigenome editing, base editing, and prime editing. Epigenome editing employed epi-effectors to manipulate chromatin structure, while base editing uses base editors to engineer precise changes for trait improvement. Newer technologies such as prime editing have now been developed as a “search-and-replace” tool to engineer all possible single-base changes. Owing to the availability of these, the field of genome editing has evolved rapidly to develop crop plants with improved traits. In this review, we present the evolution of the CRISPR/Cas system into new-age methods of genome engineering across various plant species and the impact they have had on tweaking plant genomes and associated outcomes on crop improvement initiatives.
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Affiliation(s)
- Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), México-Veracruz, Mexico
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
| | - Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Alquézar B, Bennici S, Carmona L, Gentile A, Peña L. Generation of Transfer-DNA-Free Base-Edited Citrus Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:835282. [PMID: 35371165 PMCID: PMC8965368 DOI: 10.3389/fpls.2022.835282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
To recover transgenic citrus plants in the most efficient manner, the use of selection marker genes is essential. In this work, it was shown that the mutated forms of the acetolactate synthase (ALS) gene in combination with the herbicide selection agent imazapyr (IMZ) added to the selection medium may be used to achieve this goal. This approach enables the development of cisgenic regenerants, namely, plants without the incorporation of those bacterial genes currently employed for transgenic selection, and additionally it allows the generation of edited, non-transgenic plants with altered endogenous ALS genes leading to IMZ resistance. In this work, the citrus mutants, in which ALS has been converted into IMZ-resistant forms using a base editor system, were recovered after cocultivation of the explants with Agrobacterium tumefaciens carrying a cytidine deaminase fused to nSpCas9 in the T-DNA and selecting regenerants in the culture medium supplemented with IMZ. Analysis of transgene-free plants indicated that the transient expression of the T-DNA genes was sufficient to induce ALS mutations and thus generate IMZ-resistant shoots at 11.7% frequency. To our knowledge, this is the first report of T-DNA-free edited citrus plants. Although further optimization is required to increase edition efficiency, this methodology will allow generating new citrus varieties with improved organoleptic/agronomic features without the need to use foreign genes.
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Affiliation(s)
- Berta Alquézar
- Laboratório de Biotecnologia Vegetal, Pesquisa, and Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Stefania Bennici
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Lourdes Carmona
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Alessandra Gentile
- Department of Agriculture, Food, and Environment, University of Catania, Catania, Italy
| | - Leandro Peña
- Laboratório de Biotecnologia Vegetal, Pesquisa, and Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
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Huang X, Wang Y, Wang N. Base Editors for Citrus Gene Editing. Front Genome Ed 2022; 4:852867. [PMID: 35296063 PMCID: PMC8919994 DOI: 10.3389/fgeed.2022.852867] [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: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022] Open
Abstract
Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.
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Schröpfer S, Lempe J, Emeriewen OF, Flachowsky H. Recent Developments and Strategies for the Application of Agrobacterium-Mediated Transformation of Apple Malus × domestica Borkh. FRONTIERS IN PLANT SCIENCE 2022; 13:928292. [PMID: 35845652 PMCID: PMC9280197 DOI: 10.3389/fpls.2022.928292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/08/2022] [Indexed: 05/09/2023]
Abstract
Genetic transformation has become an important tool in plant genome research over the last three decades. This applies not only to model plants such as Arabidopsis thaliana but also increasingly to cultivated plants, where the establishment of transformation methods could still pose many problems. One of such plants is the apple (Malus spp.), the most important fruit of the temperate climate zone. Although the genetic transformation of apple using Agrobacterium tumefaciens has been possible since 1989, only a few research groups worldwide have successfully applied this technology, and efficiency remains poor. Nevertheless, there have been some developments, especially in recent years, which allowed for the expansion of the toolbox of breeders and breeding researchers. This review article attempts to summarize recent developments in the Agrobacterium-mediated transformation strategies of apple. In addition to the use of different tissues and media for transformation, agroinfiltration, as well as pre-transformation with a Baby boom transcription factor are notable successes that have improved transformation efficiency in apple. Further, we highlight targeted gene silencing applications. Besides the classical strategies of RNAi-based silencing by stable transformation with hairpin gene constructs, optimized protocols for virus-induced gene silencing (VIGS) and artificial micro RNAs (amiRNAs) have emerged as powerful technologies for silencing genes of interest. Success has also been achieved in establishing methods for targeted genome editing (GE). For example, it was recently possible for the first time to generate a homohistont GE line into which a biallelic mutation was specifically inserted in a target gene. In addition to these methods, which are primarily aimed at increasing transformation efficiency, improving the precision of genetic modification and reducing the time required, methods are also discussed in which genetically modified plants are used for breeding purposes. In particular, the current state of the rapid crop cycle breeding system and its applications will be presented.
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Abdallah NA, Hamwieh A, Radwan K, Fouad N, Prakash C. Genome editing techniques in plants: a comprehensive review and future prospects toward zero hunger. GM CROPS & FOOD 2021; 12:601-615. [PMID: 35135438 PMCID: PMC9208631 DOI: 10.1080/21645698.2021.2021724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Promoting sustainable agriculture and improving nutrition are the main united nation sustainable development goals by 2030. New technologies are required to achieve zero hunger, and genome editing technology is the most promising one. In the last decade, genome editing (GE) using the CRISPR/Cas system has attracted researchers as a safer and easy tool for genome editing in several living organisms. GE has revolutionized the field of agriculture by improving biotic and abiotic stresses and yield improvement. GE technologies were developed fast lately to avoid the obstacles that face GM crops. GE technology, depending on site directed nuclease (SDN), is divided into three categories according to the modification methods. Developing transgenic-free edited plants without introducing foreign DNA meet the acceptance and regulatory ratification of several countries. There are several ongoing efforts from different countries that are rapidly expanding to adopt the current technological innovations. This review summarizes the different GE technologies and their application as a way to help in ending hunger.
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Affiliation(s)
- Naglaa A. Abdallah
- Department of Genetics Faculty of Agriculture, Cairo University, Cairo, Egypt
- National Biotechnology Network of Expertise, ASRT, Egypt
| | - Aladdin Hamwieh
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled Radwan
- National Biotechnology Network of Expertise, ASRT, Egypt
- Department of Biotechnology, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Nourhan Fouad
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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22
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Schröpfer S, Flachowsky H. Tracing CRISPR/Cas12a Mediated Genome Editing Events in Apple Using High-Throughput Genotyping by PCR Capillary Gel Electrophoresis. Int J Mol Sci 2021; 22:ijms222212611. [PMID: 34830492 PMCID: PMC8619667 DOI: 10.3390/ijms222212611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023] Open
Abstract
The use of the novel CRISPR/Cas12a system is advantageous, as it expands the possibilities for genome editing (GE) applications due to its different features compared to the commonly used CRISPR/Cas9 system. In this work, the CRISPR/Cas12a system was applied for the first time to apple to investigate its general usability for GE applications. Efficient guide RNAs targeting different exons of the endogenous reporter gene MdPDS, whose disruption leads to the albino phenotype, were pre-selected by in vitro cleavage assays. A construct was transferred to apple encoding for a CRISPR/Cas12a system that simultaneously targets two loci in MdPDS. Using fluorescent PCR capillary electrophoresis and amplicon deep sequencing, all identified GE events of regenerated albino shoots were characterized as deletions. Large deletions between the two neighboring target sites were not observed. Furthermore, a chimeric composition of regenerates and shoots that exhibited multiple GE events was observed frequently. By comparing both analytical methods, it was shown that fluorescent PCR capillary gel electrophoresis is a sensitive high-throughput genotyping method that allows accurate predictions of the size and proportion of indel mutations for multiple loci simultaneously. Especially for species exhibiting high frequencies of chimerism, it can be recommended as a cost-effective method for efficient selection of homohistont GE lines.
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23
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Savadi S, Mangalassery S, Sandesh MS. Advances in genomics and genome editing for breeding next generation of fruit and nut crops. Genomics 2021; 113:3718-3734. [PMID: 34517092 DOI: 10.1016/j.ygeno.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/21/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India.
| | | | - M S Sandesh
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India
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Molla KA, Sretenovic S, Bansal KC, Qi Y. Precise plant genome editing using base editors and prime editors. NATURE PLANTS 2021; 7:1166-1187. [PMID: 34518669 DOI: 10.1038/s41477-021-00991-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 05/06/2023]
Abstract
The development of CRISPR-Cas systems has sparked a genome editing revolution in plant genetics and breeding. These sequence-specific RNA-guided nucleases can induce DNA double-stranded breaks, resulting in mutations by imprecise non-homologous end joining (NHEJ) repair or precise DNA sequence replacement by homology-directed repair (HDR). However, HDR is highly inefficient in many plant species, which has greatly limited precise genome editing in plants. To fill the vital gap in precision editing, base editing and prime editing technologies have recently been developed and demonstrated in numerous plant species. These technologies, which are mainly based on Cas9 nickases, can introduce precise changes into the target genome at a single-base resolution. This Review provides a timely overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.
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Affiliation(s)
- Kutubuddin A Molla
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India.
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Kailash C Bansal
- The Alliance of Bioversity International and the International Centre for Tropical Agriculture, Asia-India, New Delhi, India
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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Sattar MN, Iqbal Z, Al-Khayri JM, Jain SM. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. PLANTS (BASEL, SWITZERLAND) 2021; 10:1347. [PMID: 34371550 PMCID: PMC8309169 DOI: 10.3390/plants10071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022]
Abstract
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.
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Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - S. Mohan Jain
- Department of Agricultural Sciences, PL-27, University of Helsinki, 00014 Helsinki, Finland;
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Favero BT, Tan Y, Lin Y, Hansen HB, Shadmani N, Xu J, He J, Müller R, Almeida A, Lütken H. Transgenic Kalanchoë blossfeldiana, Containing Individual rol Genes and Open Reading Frames Under 35S Promoter, Exhibit Compact Habit, Reduced Plant Growth, and Altered Ethylene Tolerance in Flowers. FRONTIERS IN PLANT SCIENCE 2021; 12:672023. [PMID: 34025708 PMCID: PMC8138453 DOI: 10.3389/fpls.2021.672023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Reduced growth habit is a desirable trait for ornamental potted plants and can successfully be obtained through Rhizobium rhizogenes transformation in a stable and heritable manner. Additionally, it can also be obtained by transformation with Agrobacterium tumefaciens harboring specific genes from R. rhizogenes. The bacterial T-DNA harbors four root oncogenic loci (rol) genes and 14 less known open reading frames (ORFs). The four rol genes, i.e., rolA, rolB, rolC, and rolD, are conceived as the common denominator for the compact phenotype and the other less characterized ORFs seem auxiliary but present a potential breeding target for less aberrant and/or more tailored phenotypes. In this study, Kalanchoë blossfeldiana 'Molly' was transformed with individual rol genes and selected ORFs in 35S overexpressing cassettes to comprehensively characterize growth traits, gene copy and expression, and ethylene tolerance of the flowers. An association of reduced growth habit, e.g. height and diameter, was observed for rolB2 and ORF14-2 when a transgene single copy and high gene expression were detected. Chlorophyll content was reduced in overexpressing lines compared to wild type (WT), except for one ΔORF13a (a truncated ORF13a, where SPXX DNA-binding motif is absent). The flower number severely decreased in the overexpressing lines compared to WT. The anthesis timing showed that WT opened the first flower at 68.9 ± 0.9 days and the overexpressing lines showed similar or up to 24 days delay in flowering. In general, a single or low relative gene copy insertion was correlated to higher gene expression, ca. 3 to 5-fold, in rolB and ΔORF13a lines, while in ORF14 such relation was not directly linked. The increased gene expression observed in rolB2 and ΔORF13a-2 contributed to reducing plant growth and a more compact habit. Tolerance of detached flowers to 0.5 μl L-1 ethylene was markedly higher for ORF14 with 66% less flower closure at day 3 compared to WT. The subcellular localization of rolC and ΔORF13a was investigated by transient expression in Nicotiana benthamiana and confocal images showed that rolC and ΔORF13a are soluble and localize in the cytoplasm being able to enter the nucleus.
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Affiliation(s)
- Bruno Trevenzoli Favero
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Yi Tan
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Yan Lin
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Hanne Bøge Hansen
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Nasim Shadmani
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Jiaming Xu
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Junou He
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Renate Müller
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
| | - Aldo Almeida
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik Lütken
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Taastrup, Denmark
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