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Zhang Z, Wang W, Ali S, Luo X, Xie L. CRISPR/Cas9-Mediated Multiple Knockouts in Abscisic Acid Receptor Genes Reduced the Sensitivity to ABA during Soybean Seed Germination. Int J Mol Sci 2022; 23:ijms232416173. [PMID: 36555815 PMCID: PMC9784318 DOI: 10.3390/ijms232416173] [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: 11/12/2022] [Revised: 12/04/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Abscisic acid (ABA) is an important plant hormone that regulates numerous functions in plant growth, development, and stress responses. Several proteins regulate the ABA signal transduction mechanism in response to environmental stress. Among them, the PYR1/PYL/RCAR family act as ABA receptors. This study used the CRISPR/Cas9 gene-editing system with a single gRNA to knock out three soybean PYL genes: GmPYL17, GmPYL18, and GmPYL19. The gRNA may efficiently cause varying degrees of deletion of GmPYL17, GmPYL18, and GmPYL19 gene target sequences, according to the genotyping results of T0 plants. A subset of induced alleles was successfully transferred to progeny. In the T2 generation, we obtained double and triple mutant genotypes. At the seed germination stage, CRISPR/Cas9-created GmPYL gene knockout mutants, particularly gmpyl17/19 double mutants, are less susceptible to ABA than the wild type. RNA-Seq was used to investigate the differentially expressed genes related to the ABA response from germinated seedlings under diverse treatments using three biological replicates. The gmpyl17/19-1 double mutant was less susceptible to ABA during seed germination, and mutant plant height and branch number were higher than the wild type. Under ABA stress, the GO enrichment analysis showed that certain positive germination regulators were activated, which reduced ABA sensitivity and enhanced seed germination. This research gives a theoretical basis for a better understanding of the ABA signaling pathway and the participation of the key component at their molecular level, which helps enhance soybean abiotic stress tolerance. Furthermore, this research will aid breeders in regulating and improving soybean production and quality under various stress conditions.
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Affiliation(s)
- Zhaohan Zhang
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
| | - Wanpeng Wang
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shahid Ali
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
- Correspondence: (X.L.); (L.X.)
| | - Linan Xie
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (X.L.); (L.X.)
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Gao P, Qin L, Nguyen H, Sheng H, Quilichini TD, Xiang D, Kochian LV, Wei Y, Datla R. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9-generated diallelic mutants reveal Arabidopsis actin-related protein 2 function in the trafficking of syntaxin PEN1. FRONTIERS IN PLANT SCIENCE 2022; 13:934002. [PMID: 36204067 PMCID: PMC9531028 DOI: 10.3389/fpls.2022.934002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
In plants, the actin cytoskeleton plays a critical role in defense against diverse pathogens. The formation of actin patches is essential for the intracellular transport of organelles and molecules toward pathogen penetration sites and the formation of papillae for an early cellular response to powdery mildew attack in Arabidopsis thaliana. This response process is regulated by the actin-related protein (ARP)2/3 complex and its activator, the WAVE/SCAR complex (W/SRC). The ARP2/3 complex is also required for maintaining steady-state levels of the defense-associated protein, PENETRATION 1 (PEN1), at the plasma membrane and for its deposition into papillae. However, specific ARP2 functionalities in this context remain unresolved, as knockout mutants expressing GFP-PEN1 reporter constructs could not be obtained by conventional crossing approaches. In this study, employing a CRISPR/Cas9 multiplexing-mediated genome editing approach, we produced an ARP2 knockout expressing the GFP-PEN1 marker in Arabidopsis. This study successfully identified diallelic somatic mutations with both ARP2 alleles edited among the primary T1 transgenic plants, and also obtained independent lines with stable arp2/arp2 mutations in the T2 generation. Further analyses on these arp2/arp2 mutants showed similar biological functions of ARP2 to ARP3 in the accumulation of PEN1 against fungal invasion. Together, this CRISPR/Cas9-based approach offers highly efficient simultaneous disruption of the two ARP2 alleles in GFP-PEN1-expressing lines, and a rapid method for performing live-cell imaging to facilitate the investigation of important plant-pathogen interactions using a well-established and widely applied GFP marker system, thus gaining insights and elucidating the contributions of ARP2 upon fungal attack.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Li Qin
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hanh Nguyen
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Huajin Sheng
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Teagen D. Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yangdou Wei
- College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Application of CRISPR/Cas9 System for Efficient Gene Editing in Peanut. PLANTS 2022; 11:plants11101361. [PMID: 35631786 PMCID: PMC9144340 DOI: 10.3390/plants11101361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
Peanuts are an economically important crop cultivated worldwide. However, several limitations restrained its productivity, including biotic/abiotic stresses. CRISPR/Cas9-based gene-editing technology holds a promising approach to developing new crops with improved agronomic and nutritional traits. Its application has been successful in many important crops. However, the application of this technology in peanut research is limited, probably due to the lack of suitable constructs and protocols. In this study, two different constructs were generated to induce insertion/deletion mutations in the targeted gene for a loss of function study. The first construct harbors the regular gRNA scaffold, while the second construct has the extended scaffold plus terminator. The designed gRNA targeting the coding sequence of the FAD2 genes was cloned into both constructs, and their functionality and efficiency were validated using the hairy root transformation system. Both constructs displayed insertions and deletions as the types of edits. The construct harboring the extended plus gRNA terminator showed a higher editing efficiency than the regular scaffold for monoallelic and biallelic mutations. These two constructs can be used for gene editing in peanuts and could provide tools for improving peanut lines for the benefit of peanut breeders, farmers, and industry.
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Giudice G, Moffa L, Varotto S, Cardone MF, Bergamini C, De Lorenzis G, Velasco R, Nerva L, Chitarra W. Novel and emerging biotechnological crop protection approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1495-1510. [PMID: 33945200 PMCID: PMC8384607 DOI: 10.1111/pbi.13605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
Traditional breeding or genetically modified organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe force scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. In addition, we take into consideration a toolbox of new techniques based on applications of RNA interference and epigenome modifications, which can be adopted for improving plant resilience. Recent advances in these biotechnological applications are mainly reported for non-model plants and woody crops in particular. Indeed, the characterization of RNAi machinery in plants is fundamental to transform available information into biologically or biotechnologically applicable knowledge. Finally, here we discuss how these innovative and environmentally friendly techniques combined with traditional breeding can sustain a modern agriculture and be of potential contribution to climate change mitigation.
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Affiliation(s)
- Gaetano Giudice
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Loredana Moffa
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A)University of UdineUdineItaly
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE)University of PadovaLegnaroPDItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Riccardo Velasco
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
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Shipman EN, Yu J, Zhou J, Albornoz K, Beckles DM. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? HORTICULTURE RESEARCH 2021; 8:1. [PMID: 33384412 PMCID: PMC7775472 DOI: 10.1038/s41438-020-00428-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/22/2023]
Abstract
Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR-Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are "ripe" for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5-10 years.
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Affiliation(s)
- Emma N Shipman
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA.
| | - Jingwei Yu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Karin Albornoz
- Departamento de Produccion Vegetal, Universidad de Concepcion, Region del BioBio, Concepcion, Chile.
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. PLANT METHODS 2019; 15:119. [PMID: 31673276 PMCID: PMC6814032 DOI: 10.1186/s13007-019-0500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgRNA) and the CRISPR/Cas9 system, small editing events such as deletions of few bases can be obtained. However larger deletions are required for some applications. In addition, identification and characterization of edited events can be challenging in plants with complex genomes, such as wheat. RESULTS In this study, we used the CRISPR/Cas9 system and developed a protocol that yielded high number of large deletions employing a pair of co-expressed sgRNA to target the same gene. The protocol was validated by targeting three genes, TaABCC6, TaNFXL1 and TansLTP9.4 in a wheat protoplast assay. Deletions of sequences located between the two sgRNA in each gene were the most frequent editing events observed for two of the three genes. A comparative assessment of editing frequencies between a codon-optimized Cas9 for expression in algae, crCas9, and a plant codon-optimized Cas9, pcoCas9, showed more consistent results with the vector expressing pcoCas9. Editing of TaNFXL1 by co-expression of sgRNA pair was investigated in transgenic wheat plants. Given the ploidy of bread wheat, a rapid, robust and inexpensive genotyping protocol was also adapted for hexaploid genomes and shown to be a useful tool to identify homoeolog-specific editing events in wheat. CONCLUSIONS Co-expressed pairs of sgRNA targeting single genes in conjunction with the CRISPR/Cas9 system produced large deletions in wheat. In addition, a genotyping protocol to identify editing events in homoeologs of TaNFXL1 was successfully adapted.
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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