1
|
Ishii K, Kazama Y, Hirano T, Fawcett JA, Sato M, Hirai MY, Sakai F, Shirakawa Y, Ohbu S, Abe T. Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1352564. [PMID: 38693931 PMCID: PMC11061394 DOI: 10.3389/fpls.2024.1352564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/11/2024] [Indexed: 05/03/2024]
Abstract
Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome.
Collapse
Affiliation(s)
- Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Radiation Measurement and Dose Assessment, Institute for Radiological Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Japan
| | - Tomonari Hirano
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jeffrey A. Fawcett
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), Wako, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | | | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Sumie Ohbu
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| |
Collapse
|
2
|
Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
Collapse
Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| |
Collapse
|
3
|
Ali E, Zhang K. CRISPR-mediated technology for seed oil improvement in rapeseed: Challenges and future perspectives. FRONTIERS IN PLANT SCIENCE 2023; 14:1086847. [PMID: 37025135 PMCID: PMC10070842 DOI: 10.3389/fpls.2023.1086847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Rapeseed not only provide considerable amount of edible oil with high nutritional properties but can also be used as a raw material for biofuel production in many industries. It is therefore in high demand to bring genetic changes in order to fulfill the need of human and of industries. Though traditional breeding techniques such as hybridization and mutagenesis remained the top methods for long time to create improved varieties in oilseed rape. Clustered regularly interspaced short palindromic repeats (CRISPR) is becoming one of the most valuable gene editing technologies that allow precise genome engineering, and open new ways for research in plant functional genomics. Though CRISPR has been used in many other crops for genetic improvement it is expected to be an effective tool for genome editing and molecular design in oilseed rape for seed oil improvement. This mini review will discuss and summarize the past and ongoing research and development in rapeseed in terms of seed oil improvement and fatty acid composition using CRISPR technology. In addition, the factors that hinder the efficiency of this tool and how to eliminate those factors will be briefly summarized. The improvement of CRISPR technology for getting better results in oilseed rape will also be considered here. This minireview will open new windows for researchers in Brassica napus oil improvement research and genetic improvement using CRISPR technology.
Collapse
Affiliation(s)
- Essa Ali
- *Correspondence: Kewei Zhang, ; Essa Ali,
| | | |
Collapse
|
4
|
CRISPR-Based Genome Editing: Advancements and Opportunities for Rice Improvement. Int J Mol Sci 2022; 23:ijms23084454. [PMID: 35457271 PMCID: PMC9027422 DOI: 10.3390/ijms23084454] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
To increase the potentiality of crop production for future food security, new technologies for plant breeding are required, including genome editing technology—being one of the most promising. Genome editing with the CRISPR/Cas system has attracted researchers in the last decade as a safer and easier tool for genome editing in a variety of living organisms including rice. Genome editing has transformed agriculture by reducing biotic and abiotic stresses and increasing yield. Recently, genome editing technologies have been developed quickly in order to avoid the challenges that genetically modified crops face. Developing transgenic-free edited plants without introducing foreign DNA has received regulatory approval in a number of countries. Several ongoing efforts from various countries are rapidly expanding to adopt the innovations. This review covers the mechanisms of CRISPR/Cas9, comparisons of CRISPR/Cas9 with other gene-editing technologies—including newly emerged Cas variants—and focuses on CRISPR/Cas9-targeted genes for rice crop improvement. We have further highlighted CRISPR/Cas9 vector construction model design and different bioinformatics tools for target site selection.
Collapse
|
5
|
Matsuo K. CRISPR/Cas9-mediated knockout of the DCL2 and DCL4 genes in Nicotiana benthamiana and its productivity of recombinant proteins. PLANT CELL REPORTS 2022; 41:307-317. [PMID: 34783883 DOI: 10.1007/s00299-021-02809-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE DCL2 and DCL4 genes in Nicotiana benthamiana plants were successfully edited using the CRISPR/Cas9 system. Recently, plants have been utilized for recombinant protein production similar to other expression systems, i.e., bacteria, yeast, insect, and mammal cells. However, insufficient amounts of recombinant proteins are often produced in plant cells. The repression of RNA silencing within plant cells could improve production levels of recombinant protein because RNA silencing frequently decomposes mRNAs from transgenes. In this study, the genes dicer-like protein 2 and 4 (NbDCL2 and NbDCL4) were successfully edited to produce double-knockout transgenic Nicotiana benthamiana plants (dcl2dcl4 plants) using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology. A transient green fluorescent protein (GFP) gene expression assay revealed that the dcl2dcl4 plants accumulated higher amounts of GFP and GFP mRNA than wild type (WT) and RNA-dependent RNA polymerase 6-knockout N. benthamiana plants (ΔRDR6 plants). Small RNA sequencing also showed that dcl2dcl4 plants accumulated lower amounts of small interfering RNAs (siRNAs) against the GFP gene than WT plants. The dcl2dcl4 plants might also produce higher amounts of human fibroblast growth factor 1 (FGF1) than WT and ΔRDR6 plants. These observations appear to reflect differences between DCLs and RDR6 in plant cell biological mechanisms. These results reveal that dcl2dcl4 plants would be suitable as platform plants for recombinant protein production.
Collapse
Affiliation(s)
- Kouki Matsuo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
De Bruyn C, Ruttink T, Eeckhaut T, Jacobs T, De Keyser E, Goossens A, Van Laere K. Establishment of CRISPR/Cas9 Genome Editing in Witloof (Cichorium intybus var. foliosum). Front Genome Ed 2020; 2:604876. [PMID: 34713228 PMCID: PMC8525355 DOI: 10.3389/fgeed.2020.604876] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/24/2020] [Indexed: 01/09/2023] Open
Abstract
Cichorium intybus var. foliosum (witloof) is an economically important crop with a high nutritional value thanks to many specialized metabolites, such as polyphenols and terpenoids. However, witloof plants are rich in sesquiterpene lactones (SL) which are important for plant defense but also impart a bitter taste, thus limiting industrial applications. Inactivating specific genes in the SL biosynthesis pathway could lead to changes in the SL metabolite content and result in altered bitterness. In this study, a CRISPR/Cas9 genome editing workflow was implemented for witloof, starting with polyethylene glycol (PEG) mediated protoplast transfection for CRISPR/Cas9 vector delivery, followed by whole plant regeneration and mutation analysis. Protoplast transfection efficiencies ranged from 20 to 26 %. A CRISPR/Cas9 vector targeting the first exon of the phytoene desaturase (CiPDS) gene was transfected into witloof protoplasts and resulted in the knockout of CiPDS, giving rise to an albino phenotype in 23% of the regenerated plants. Further implementing our protocol, the SL biosynthesis pathway genes germacrene A synthase (GAS), germacrene A oxidase (GAO), and costunolide synthase (COS) were targeted in independent experiments. Highly multiplex (HiPlex) amplicon sequencing of the genomic target loci revealed plant mutation frequencies of 27.3, 42.7, and 98.3% in regenerated plants transfected with a CRISPR/Cas9 vector targeting CiGAS, CiGAO, and CiCOS, respectively. We observed different mutation spectra across the loci, ranging from consistently the same +1 nucleotide insertion in CiCOS across independent mutated lines, to a complex set of 20 mutation types in CiGAO across independent mutated lines. These results demonstrate a straightforward workflow for genome editing based on transfection and regeneration of witloof protoplasts and subsequent HiPlex amplicon sequencing. Our CRISPR/Cas9 workflow can enable gene functional research and faster incorporation of novel traits in elite witloof lines in the future, thus facilitating the development of novel industrial applications for witloof.
Collapse
Affiliation(s)
- Charlotte De Bruyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
- *Correspondence: Charlotte De Bruyn
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Eeckhaut
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Thomas Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
| | - Ellen De Keyser
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
| | - Katrijn Van Laere
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| |
Collapse
|
8
|
Wenjing W, Chen Q, Singh PK, Huang Y, Pei D. CRISPR/Cas9 edited HSFA6a and HSFA6b of Arabidopsis thaliana offers ABA and osmotic stress insensitivity by modulation of ROS homeostasis. PLANT SIGNALING & BEHAVIOR 2020; 15:1816321. [PMID: 32936726 PMCID: PMC7671043 DOI: 10.1080/15592324.2020.1816321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 05/21/2023]
Abstract
The role of Heat Shock Transcription Factor 6 (HSFA6a & HSFA6b) in response to abiotic stresses such as ABA, drought, salinity, drought, and osmotic stress is individually well established. Unfortunately, the functional redundancy between the HSFA6a and HSFA6b as well as the consequences of simultaneous editing of both in response to aforementioned stresses remains elusive. Therefore, this study was designed with the aim of addressing whether there is any functional redundancy between HSFA6a and HSFA6b as well as to decipher their role in abiotic stresses tolerance in Arabidopsis thaliana, by using the CRISPR-Cas9. We have generated the single (hsfa6a and hsfa6b) as well as double mutants (hsfa6a/hsfa6b-1 and hsfa6a/hsfa6b-2) of HSFA6a and HSFA6b with higher frequencies of deletion, insertion, and substitution. The phenotypic characterization of generated double and single mutants under abiotic stresses such as ABA, mannitol, and NaCl identified double mutants more tolerant to subjected abiotic stresses than those of their single mutants. It warrants mentioning that we have identified that HSFA6a and HSFA6b also involved in other major ABA responses, including ABA-inhibited seed germination, stomatal movement, and water loss. In addition to the above, the simultaneous editing of HSFA6a and HSFA6b lead to a reduced ROS accumulation, accompanied by increased expression of much abiotic stress and ABA-responsive genes, including involved in regulation of ROS level. In conclusion, these results suggest that HSFA6a and HSFA6b may offer abiotic stress tolerance by regulating the ROS homeostasis in plants.
Collapse
Affiliation(s)
- Wang Wenjing
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
| | - Qingbin Chen
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
| | - Prashant Kumar Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
- Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, India
| | - Yuanyuan Huang
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
| | - Dongli Pei
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
- CONTACT Dongli Pei Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, 476000, China
| |
Collapse
|
9
|
Shan S, Soltis PS, Soltis DE, Yang B. Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11314. [PMID: 31993256 PMCID: PMC6976890 DOI: 10.1002/aps3.11314] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/26/2019] [Indexed: 05/03/2023]
Abstract
The past six years have seen the rapid growth of studies of CRISPR/Cas9 in plant genome editing, a method that enormously facilitates both basic research and practical applications. Most studies have focused on genetic model species, but plant species that are not genetic models may also be economically important or biologically significant, or both. However, developing the CRISPR/Cas9 system in a nongenetic model is challenging. Here, we summarize CRISPR/Cas9 applications in 45 plant genera across 24 families and provide a reference for practical application of CRISPR in nongenetic model plant systems. Suggestions for selecting plant species and target genes are given for proof-of-principle CRISPR studies, and the processes of vector construction are reviewed. We recommend using transient assays to identify a desired CRISPR/Cas9 system in a nongenetic model. We then review methods of plant transformation and describe approaches, using regenerated transgenic plants, for evaluating CRISPR editing results. Lastly, potential future applications of CRISPR in nongenetic model plant species are discussed. This review provides a road map for developing CRISPR in nongenetic models, an application that holds enormous potential in plant biology.
Collapse
Affiliation(s)
- Shengchen Shan
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
| | - Pamela S. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
| | - Douglas E. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611‐8525USA
| | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMissouri65211USA
- Donald Danforth Plant Science CenterSt. LouisMissouri63132USA
| |
Collapse
|
10
|
Chandra AK, Kumar A, Bharati A, Joshi R, Agrawal A, Kumar S. Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops. 3 Biotech 2020; 10:2. [PMID: 31824813 DOI: 10.1007/s13205-019-1994-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
Both human and animals, for their nutritional requirements, mainly rely on the plant-based foods, which provide a wide range of nutrients. Minerals, proteins, vitamins are among the nutrients which are essential and need to be available in adequate amount in edible portion of the staple crops. Increasing nutritional content in staple crops either through agronomic biofortification or through conventional plant-breeding strategies continue to be a huge task for scientists around the globe. Although some success has been achieved in recent past, in most cases, we have fallen short of expected targets. To maximize the nutrient uptake and partitioning to different economic part of plants, scientists have employed and tailored several biofortification strategies. But in present agricultural and environmental concerns, these approaches are not much effective. Henceforth, we are highlighting the recent developments and promising aspects of microbial-assisted and genomic-assisted breeding as candidate biofortification approach, that have contributed significantly in increasing nutritional content in grains of different crops. The methods used to date to accomplish nutrient enrichment with recently emerging strategies that we believe could be the most promising and holistic approach for future biofortification program. Results are encouraging, but for future perspective, the existing knowledge about the strategies needs to be confined. Concerted scientific investment are required to widen up these biofortification strategies, so that it could play an important role in ensuring nutritional security of ever-growing population in growing agricultural and environmental constraints.
Collapse
|
11
|
Handayani T, Gilani SA, Watanabe KN. Climatic changes and potatoes: How can we cope with the abiotic stresses? BREEDING SCIENCE 2019; 69:545-563. [PMID: 31988619 PMCID: PMC6977456 DOI: 10.1270/jsbbs.19070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/10/2019] [Indexed: 05/06/2023]
Abstract
Climate change triggers increases in temperature, drought, and/or salinity that threaten potato production, because they necessitate specific amounts and quality of water, meanwhile lower temperatures generally support stable crop yields. Various cultivation techniques have been developed to reduce the negative effects of drought, heat and/or salinity stresses on potato. Developing innovative varieties with relevant tolerance to abiotic stress is absolutely necessary to guarantee competitive production under sub-optimal environments. Commercial varieties are sensitive to abiotic stresses, and substantial changes to their higher tolerance levels are not easily achieved because their genetic base is narrow. Nonetheless, there are several other possibilities for genetic enhancement using landraces and wild relatives. The complexity of polysomic genetics and heterozygosity in potato hamper the phenotype evaluation over abiotic stresses and consequent conventional introgression of tolerance traits, which are more challenging than previous successes shown over diseases and insects resistances. Today, potatoes face more challenges with severe abiotic stresses. Potato wild relatives can be explored further using innovative genomic, transcriptomic, proteomic, and metabolomic approaches. At the field level, appropriate cultivation techniques must be applied along with precision farming technology and tolerant varieties developed from various breeding techniques, in order to realize high yield under multiple stresses.
Collapse
Affiliation(s)
- Tri Handayani
- Graduate School of Life & Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Indonesian Vegetable Research Institute,
Jl. Tangkuban Perahu 517, Lembang, West Bandung, West Java, 40391,
Indonesia
| | - Syed Abdullah Gilani
- Department of Biological Sciences and Chemistry, University of Nizwa,
P. O. Box 33, PC 616, Birkat Al Mouz, Nizwa,
Sultanate of Oman
| | - Kazuo N. Watanabe
- Tsukuba-Plant Innovation Research Center, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
12
|
Sood S, Joshi DC, Chandra AK, Kumar A. Phenomics and genomics of finger millet: current status and future prospects. PLANTA 2019; 250:731-751. [PMID: 30968267 DOI: 10.1007/s00425-019-03159-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Diverse gene pool, advanced plant phenomics and genomics methods enhanced genetic gain and understanding of important agronomic, adaptation and nutritional traits in finger millet. Finger millet (Eleusine coracana L. Gaertn) is an important minor millet for food and nutritional security in semi-arid regions of the world. The crop has wide adaptability and can be grown right from high hills in Himalayan region to coastal plains. It provides food grain as well as palatable straw for cattle, and is fairly climate resilient. The crop has large gene pool with distinct features of both Indian and African germplasm types. Interspecific hybridization between Indian and African germplasm has resulted in greater yield enhancement and disease resistance. The crop has shown numerous advantages over major cereals in terms of stress adaptation, nutritional quality and health benefits. It has indispensable repository of novel genes for the benefits of mankind. Although rapid strides have been made in allele mining in model crops and major cereals, the progress in finger millet genomics is lacking. Comparative genomics have paved the way for the marker-assisted selection, where resistance gene homologues of rice for blast and sequence variants for nutritional traits from other cereals have been invariably used. Transcriptomics studies have provided preliminary understanding of the nutritional variation, drought and salinity tolerance. However, the genetics of many important traits in finger millet is poorly understood and need systematic efforts from biologists across disciplines. Recently, deciphered finger millet genome will enable identification of candidate genes for agronomically and nutritionally important traits. Further, improvement in genome assembly and application of genomic selection as well as genome editing in near future will provide plethora of information and opportunity to understand the genetics of complex traits.
Collapse
Affiliation(s)
- Salej Sood
- ICAR-Central Potato Research Institute, Shimla, HP, India.
| | - Dinesh C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
| | - Ajay Kumar Chandra
- GB Pant University of Agricultural Sciences and Technology, Pantnagar, Uttarakhand, India
| | - Anil Kumar
- GB Pant University of Agricultural Sciences and Technology, Pantnagar, Uttarakhand, India.
- Rani Lakshmi Bai Central Agricultural University, Jhanshi, UP, India.
| |
Collapse
|
13
|
Matsuo K, Atsumi G. CRISPR/Cas9-mediated knockout of the RDR6 gene in Nicotiana benthamiana for efficient transient expression of recombinant proteins. PLANTA 2019; 250:463-473. [PMID: 31065786 DOI: 10.1007/s00425-019-03180-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 05/27/2023]
Abstract
MAIN CONCLUSION RDR6 gene knockout Nicotiana benthamiana plant was successfully produced using CRISPR/Cas9 technology. The production of recombinant proteins in plants has many advantages, such as safety and reduced costs. However, there are several problems with this technology, especially low levels of protein production. The dysfunction of the RNA silencing mechanism in plant cells would be effective to improve recombinant protein production because the RNA silencing mechanism efficiently degrades transgene-derived mRNAs. Therefore, to overcome this problem, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology was used to develop RNA silencing-related gene knockout transgenic Nicotiana benthamiana. We successfully produced RNA-dependent RNA polymerase 6 (RDR6), one of the most important components of the RNA silencing mechanism-knockout N. benthamiana (ΔRDR6 plants). The ΔRDR6 plants had abnormal flowers and were sterile, as with the Arabidopsis RDR6 mutants. However, a transient gene expression assay showed that the ΔRDR6 plants accumulated larger amounts of green fluorescent protein (GFP) and GFP mRNA than the wild-type (WT) plants. Small RNA sequencing analysis revealed that levels of small interfering RNA against the GFP gene were greatly reduced in the ΔRDR6 plants, as compared to that of the WT plants. These findings demonstrate that the ΔRDR6 plants can express larger amounts of recombinant proteins than WT plants and, therefore, would be useful for recombinant protein production and understanding the contributions of RDR6 to genetic and physiological events in plants.
Collapse
Affiliation(s)
- Kouki Matsuo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan.
| | - Go Atsumi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
| |
Collapse
|
14
|
Eckerstorfer MF, Dolezel M, Heissenberger A, Miklau M, Reichenbecher W, Steinbrecher RA, Waßmann F. An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs). Front Bioeng Biotechnol 2019; 7:31. [PMID: 30891445 PMCID: PMC6413072 DOI: 10.3389/fbioe.2019.00031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.
Collapse
Affiliation(s)
| | - Marion Dolezel
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | | | - Marianne Miklau
- Department Landuse & Biosafety, Environment Agency Austria, Vienna, Austria
| | - Wolfram Reichenbecher
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
| | | | - Friedrich Waßmann
- Department GMO Regulation, Biosafety, Federal Agency for Nature Conservation, Bonn, Germany
| |
Collapse
|
15
|
Fiaz S, Ahmad S, Noor MA, Wang X, Younas A, Riaz A, Riaz A, Ali F. Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities. Int J Mol Sci 2019; 20:E888. [PMID: 30791357 PMCID: PMC6412304 DOI: 10.3390/ijms20040888] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/07/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.
Collapse
Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China.
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan.
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Fahad Ali
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| |
Collapse
|
16
|
Sedeek KEM, Mahas A, Mahfouz M. Plant Genome Engineering for Targeted Improvement of Crop Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:114. [PMID: 30809237 PMCID: PMC6379297 DOI: 10.3389/fpls.2019.00114] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.
Collapse
Affiliation(s)
| | | | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
17
|
Zhang K, Nie L, Cheng Q, Yin Y, Chen K, Qi F, Zou D, Liu H, Zhao W, Wang B, Li M. Effective editing for lysophosphatidic acid acyltransferase 2/5 in allotetraploid rapeseed ( Brassica napus L.) using CRISPR-Cas9 system. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:225. [PMID: 31548867 PMCID: PMC6753616 DOI: 10.1186/s13068-019-1567-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/11/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Brassica napus is one of the most important oilseed crops, and can supply considerable amounts of edible oil as well as provide raw materials for the production of biodiesel in the biotechnology industry. Lysophosphatidic acid acyltransferase (LPAT), a key enzyme in the Kennedy pathway, catalyses fatty acid chains into 3-phosphoglycerate and promotes further production of oil in the form of triacylglycerol. However, because B. napus is an allotetraploid with two subgenomes, the precise genes which involved in oil production remain unclear due to the intractability of efficiently knocking out all copies with high genetic redundancy. Therefore, a robust gene editing technology is necessary for gene function analysis. RESULTS An efficient gene editing technology was developed for the allotetraploid plant B. napus using the CRISPR-Cas9 system. Previous studies showed poor results in either on-target or off-target activity in B. napus. In the present study, four single-gRNAs and two multi-gRNAs were deliberately designed from the conserved coding regions of BnLPAT2 which has seven homologous genes, and BnLPAT5, which has four homologous genes. The mutation frequency was found to range from 17 to 68%, while no mutation was observed in the putative off-target sites. The seeds of the Bnlpat2/Bnlpat5 mutant were wizened and showed enlarged oil bodies, disrupted distribution of protein bodies and increased accumulation of starch in mature seeds. The oil content decreased, with an average decrease of 32% for Bnlpat2 lines and 29% for Bnlpat5 lines in single-gRNA knockout lines, and a decline of 24% for Bnlpat2 mutant lines (i.e., g123) and 39% for Bnlpat2/Bnlpat5 double mutant lines (i.e., g134) in multi-gRNA knockout lines. CONCLUSIONS Seven BnLPAT2 homologous genes and four BnLPAT5 homologous genes were cleaved completely using the CRISPR-Cas9 system, which indicated that it is effective for editing all homologous genes in allotetraploid rapeseed, despite the relatively low sequence identities of both gene families. The size of the oil bodies increased significantly while the oil content decreased, confirming that BnLPAT2 and BnLPAT5 play a role in oil biosynthesis. The present study lays a foundation for further oil production improvement in oilseed crop species.
Collapse
Affiliation(s)
- Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Liluo Nie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiqi Cheng
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fuyu Qi
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Dashan Zou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Haohao Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000 China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| |
Collapse
|
18
|
Chen W, Wang P. Molecular Analysis for Characterizing Transgenic Events. Methods Mol Biol 2019; 1864:397-410. [PMID: 30415348 DOI: 10.1007/978-1-4939-8778-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To develop a commercial trait product, a large number of transgenic events are often produced to obtain the event with desired level of expression. It is crucial to develop efficient and sensitive molecular characterization methods to advance events with stable transgene expression, free of vector backbone sequences and without major changes to the native genome caused by transgene insertion. Here, we discuss a variety of analytical tools, including quantitative PCR (qPCR), Southern blot analysis, and various sequencing technologies, which have been widely used to determine the insert copy number, presence/absence of vector backbone sequences, integrity of the T-DNA, and genomic location of the T-DNA insertion. Moreover, since the discovery of RNA interference in 1998 (Fire et al., Nature 391:806-811, 1998), RNAi has emerged as another powerful tool in in the development of a new transgenic trait for insect control. RNAi creates a double-stranded RNA duplex as the active molecule which forms a strong secondary structure, resulting in challenges for detection. In addition to molecular analysis at the DNA level, this chapter describes detection methods of the active molecules (i.e., double-stranded RNA) for RNAi-based traits.
Collapse
MESH Headings
- Biotechnology/instrumentation
- Biotechnology/methods
- Blotting, Southern
- Commerce
- Crops, Agricultural/genetics
- DNA, Bacterial/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- Genome, Plant/genetics
- Plants, Genetically Modified/genetics
- Polymerase Chain Reaction
- Quantitative Trait Loci/genetics
- RNA Interference
- RNA, Double-Stranded/analysis
- RNA, Double-Stranded/genetics
- RNA, Plant/analysis
- RNA, Plant/genetics
- Transformation, Genetic
- Transgenes/genetics
Collapse
Affiliation(s)
- Wei Chen
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA.
| | - PoHao Wang
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| |
Collapse
|
19
|
Jiang S, Shen QW. Principles of gene editing techniques and applications in animal husbandry. 3 Biotech 2019; 9:28. [PMID: 30622866 DOI: 10.1007/s13205-018-1563-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/29/2018] [Indexed: 11/30/2022] Open
Abstract
Gene editing techniques were developed chronologically, which include zinc finger nuclease, transcription activator-like effector nuclease and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas 9). In this review, the working principles of these techniques were first introduced, their advantages and disadvantages were then discussed, their application in animal husbandry were elaborated, and finally human concerns about gene editing were presented. Compared to the two former techniques, the third-generation gene editing technique CRISPR/Cas9 has higher targeting efficiency and accuracy, less off-target effect, lower cytotoxicity and lower costs for being easier for vector design and manipulation. Although some people may concern about social or ethical issues, the benefits of gene editing certainly overweigh its demerits. The three gene editing techniques have been successfully used to improve the production and quality of livestock products, animal fertility, resistance to diseases, and welfare in animal husbandry. With legislation and the development of gene editing technology per se, it anticipatable that gene editing will have a broader utilization and make our lives happier.
Collapse
Affiliation(s)
- Shengwang Jiang
- 1College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Qingwu W Shen
- 2College of Food Science and Technology, Hunan Agricultural University, Changsha, 410128 Hunan China
| |
Collapse
|
20
|
Schmidt C, Pacher M, Puchta H. DNA Break Repair in Plants and Its Application for Genome Engineering. Methods Mol Biol 2019; 1864:237-266. [PMID: 30415341 DOI: 10.1007/978-1-4939-8778-8_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome engineering is a biotechnological approach to precisely modify the genetic code of a given organism in order to change the context of an existing sequence or to create new genetic resources, e.g., for obtaining improved traits or performance. Efficient targeted genome alterations are mainly based on the induction of DNA double-strand breaks (DSBs) or adjacent single-strand breaks (SSBs). Naturally, all organisms continuously have to deal with DNA-damaging factors challenging the genetic integrity, and therefore a wide range of DNA repair mechanisms have evolved. A profound understanding of the different repair pathways is a prerequisite to control and enhance targeted gene modifications. DSB repair can take place by nonhomologous end joining (NHEJ) or homology-dependent repair (HDR). As the main outcome of NHEJ-mediated repair is accompanied by small insertions and deletions, it is applicable to specifically knock out genes or to rearrange linkage groups or whole chromosomes. The basic requirement for HDR is the presence of a homologous template; thus this process can be exploited for targeted integration of ectopic sequences into the plant genome. The development of different types of artificial site-specific nucleases allows for targeted DSB induction in the plant genome. Such synthetic nucleases have been used for both qualitatively studying DSB repair in vivo with respect to mechanistic differences and quantitatively in order to determine the role of key factors for NHEJ and HR, respectively. The conclusions drawn from these studies allow for a better understanding of genome evolution and help identifying synergistic or antagonistic genetic interactions while supporting biotechnological applications for transiently modifying the plant DNA repair machinery in favor of targeted genome engineering.
Collapse
Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
| |
Collapse
|
21
|
Fonseca PLC, Badotti F, de Oliveira TFP, Fonseca A, Vaz ABM, Tomé LMR, Abrahão JS, Marques JT, Trindade GS, Chaverri P, Aguiar ERGR, Góes-Neto A. Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus. Virol J 2018; 15:184. [PMID: 30477549 PMCID: PMC6258436 DOI: 10.1186/s12985-018-1095-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022] Open
Abstract
Background Hevea brasiliensis is an important commercial crop due to the high quality of the latex it produces; however, little is known about viral infections in this plant. The only virus described to infect H. brasiliensis until now is a Carlavirus, which was described more than 30 years ago. Virus-derived small interfering RNA (vsiRNAs) are the product of the plant’s antiviral defense triggered by dsRNA viral intermediates generated, during the replication cycle. These vsiRNAs are complementar to viral genomes and have been widely used to identify and characterize viruses in plants. Methods In the present study, we investigated the virome of leaf and sapwood samples from native H. brasiliensis trees collected in two geographic areas in the Brazilian Amazon. Small RNA (sRNA) deep sequencing and bioinformatic tools were used to assembly, identify and characterize viral contigs. Subsequently, PCR amplification techniques were performed to experimentally verify the presence of the viral sequences. Finally, the phylogenetic relationship of the putative new virus with related viral genomes was analyzed. Results Our strategy allowed the identification of 32 contigs with high similarity to viral reference genomes, from which 23 exhibited homology to viruses of the Tymoviridae family. The reads showed a predominant size distribution at 21 nt derived from both strands, which was consistent with the vsiRNAs profile. The presence and genome position of the viral contigs were experimentally confirmed using droplet digital PCR amplifications. A 1913 aa long fragment was obtained and used to infer the phylogenetic relationship of the putative new virus, which indicated that it is taxonomically related to the Grapevine fleck virus, genus Maculavirus. The putative new virus was named Hevea brasiliensis virus (HBrV) in reference to its host. Conclusion The methodological strategy applied here proved to be efficient in detecting and confirming the presence of new viral sequences on a ‘very difficult to manage’ sample. This is the second time that viral sequences, that could be ascribed as a putative novel virus, associated to the rubber tree has been identified. Electronic supplementary material The online version of this article (10.1186/s12985-018-1095-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30421-169, Brazil
| | - Tatiana F P de Oliveira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Antônio Fonseca
- LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Aline B M Vaz
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Luiz M R Tomé
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Jônatas S Abrahão
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Giliane S Trindade
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.,Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
| | - Eric R G R Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil. .,Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, BA, ,40110-100, Brazil.
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
| |
Collapse
|
22
|
Joshi DC, Sood S, Hosahatti R, Kant L, Pattanayak A, Kumar A, Yadav D, Stetter MG. From zero to hero: the past, present and future of grain amaranth breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1807-1823. [PMID: 29992369 DOI: 10.1007/s00122-018-3138-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/28/2018] [Indexed: 05/28/2023]
Abstract
Grain amaranth is an underutilized crop with high nutritional quality from the Americas. Emerging genomic and biotechnological tools are becoming available that allow the integration of novel breeding techniques for rapid improvement of amaranth and other underutilized crops. Out of thousands of edible plants, only three cereals-maize, wheat and rice-are the major food sources for a majority of people worldwide. While these crops provide high amounts of calories, they are low in protein and other essential nutrients. The dependence on only few crops, with often narrow genetic basis, leads to a high vulnerability of modern cropping systems to the predicted climate change and accompanying weather extremes. Broadening our food sources through the integration of so-called orphan crops can help to mitigate the effects of environmental change and improve qualitative food security. Thousands of traditional crops are known, but have received little attention in the last century and breeding efforts were limited. Amaranth is such an underutilized pseudocereal that is of particular interest because of its balanced amino acid and micronutrient profiles. Additionally, the C4 photosynthetic pathway and ability to withstand environmental stress make the crop a suitable choice for future agricultural systems. Despite the potential of amaranth, efforts of genetic improvement lag considerably behind those of major crops. The progress in novel breeding methods and molecular techniques developed in model plants and major crops allow a rapid improvement of underutilized crops. Here, we review the history of amaranth and recent advances in genomic tools and give a concrete perspective how novel breeding techniques can be implemented into breeding programs. Our perspectives are transferable to many underutilized crops. The implementation of these could improve the nutritional quality and climate resilience of future cropping systems.
Collapse
Affiliation(s)
- Dinesh C Joshi
- Vivekananda Institute of Hill Agriculture, Indian Council of Agricultural Research, Almora, Uttarakhand, India.
| | - Salej Sood
- Central Potato Research Institute, Indian Council of Agricultural Research, Shimla, Himachal Pradesh, India
| | - Rajashekara Hosahatti
- Vivekananda Institute of Hill Agriculture, Indian Council of Agricultural Research, Almora, Uttarakhand, India
| | - Lakshmi Kant
- Vivekananda Institute of Hill Agriculture, Indian Council of Agricultural Research, Almora, Uttarakhand, India
| | - A Pattanayak
- Vivekananda Institute of Hill Agriculture, Indian Council of Agricultural Research, Almora, Uttarakhand, India
| | - Anil Kumar
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Markus G Stetter
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, USA.
| |
Collapse
|
23
|
Singh B, Kukreja S, Goutam U. Milestones achieved in response to drought stress through reverse genetic approaches. F1000Res 2018; 7:1311. [PMID: 30631439 PMCID: PMC6290974 DOI: 10.12688/f1000research.15606.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
Drought stress is the most important abiotic stress that constrains crop production and reduces yield drastically. The germplasm of most of the cultivated crops possesses numerous unknown drought stress tolerant genes. Moreover, there are many reports suggesting that the wild species of most of the modern cultivars have abiotic stress tolerant genes. Due to climate change and population booms, food security has become a global issue. To develop drought tolerant crop varieties knowledge of various genes involved in drought stress is required. Different reverse genetic approaches such as virus-induced gene silencing (VIGS), clustered regularly interspace short palindromic repeat (CRISPR), targeting induced local lesions in genomes (TILLING) and expressed sequence tags (ESTs) have been used extensively to study the functionality of different genes involved in response to drought stress. In this review, we described the contributions of different techniques of functional genomics in the study of drought tolerant genes.
Collapse
Affiliation(s)
- Baljeet Singh
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sarvjeet Kukreja
- Department of Botany, Ch. MRM Memorial College, Sriganganagar, Rajasthan, 335804, India
| | - Umesh Goutam
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| |
Collapse
|
24
|
Silberstein DZ, Karuppanan K, Aung HH, Chen CH, Cross CE, McDonald KA. An oxidation-resistant, recombinant alpha-1 antitrypsin produced in Nicotiana benthamiana. Free Radic Biol Med 2018; 120:303-310. [PMID: 29551638 PMCID: PMC6093210 DOI: 10.1016/j.freeradbiomed.2018.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/11/2018] [Indexed: 02/08/2023]
Abstract
Proteases and reactive oxygen species (ROS) have long been implicated in playing key roles in host tissue injury at sites of inflammation dominated by macrophage activations and/or neutrophil infiltrations. Imbalances between proteases/antiproteases and ROS/antioxidants are recognized to contribute to amplification of inflammatory-based host tissue injury. This has been especially well-documented in such respiratory tract diseases as chronic obstructive pulmonary disease, cystic fibrosis, and acute respiratory distress syndrome. Inflammation-related protease/ROS disequilibria are further confounded by recognition that proteases can increase ROS by several different mechanisms and that ROS can inactivate proteases. The major human antiprotease, alpha-1 antitrypsin (AAT), is dramatically inactivated by ROS. AAT deficiency is the most prevalent genetic predisposing factor leading to emphysema, a condition treated by replacement infusions of plasma-derived AAT (hAAT) at a cost of up to $200,000 per year per patient. An updated method for production of a plant-made recombinant AAT (prAAT) engineered for enhanced oxidation resistance compared to hAAT is presented. Plant-made recombinant AAT shows comparable antiprotease activity to hAAT, and retains full activity under oxidative conditions that would deactivate hAAT. Additionally, we show that prAAT has similar effectiveness in preventing neutrophil elastase-induced cell death in an in vitro human bronchial epithelial cell culture model. We conclude that prAAT is potentially a "biobetter" AAT product that could be made available to individuals with a wide spectrum of inflammatory disorders characterized by overly aggressive neutrophilic infiltrations.
Collapse
Affiliation(s)
- David Z Silberstein
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
| | - Kalimuthu Karuppanan
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
| | - Hnin Hnin Aung
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA
| | - Ching-Hsien Chen
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA
| | - Carroll E Cross
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA; University of California, Davis, Department of Physiology and Membrane Biology, 1 Shields Ave, Davis, CA 95616, USA.
| | - Karen A McDonald
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
| |
Collapse
|
25
|
Li H, Xiao L, Zhang L, Wu J, Wei B, Sun N, Zhao Y. FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions. Front Genet 2018; 9:96. [PMID: 29675032 PMCID: PMC5896265 DOI: 10.3389/fgene.2018.00096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 03/08/2018] [Indexed: 02/01/2023] Open
Abstract
smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method. FSPP used the overlap of detected SEPs from Ribo-seq and mass spectrometry as target objects. With the expression data on transcription and translation levels, FSPP built two co-expression networks. Combing co-location relations, FSPP constructed a compound network and then annotated SEPs with functions of adjacent nodes. Tested on 38 sequenced samples of 5 human cell lines, FSPP successfully predicted 856 out of 960 annotated proteins. Interestingly, FSPP also highlighted 568 functional SEPs from these samples. After comparison, the roles predicted by FSPP were consistent with known functions. These results suggest that FSPP is a reliable tool for the identification of functional small peptides. FSPP source code can be acquired at https://www.bioinfo.org/FSPP.
Collapse
Affiliation(s)
- Hui Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Li Xiao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lili Zhang
- School of Computer and Control Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, China.,CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiarui Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Bin Wei
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ninghui Sun
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
26
|
Garcia Ruiz MT, Knapp AN, Garcia-Ruiz H. Profile of genetically modified plants authorized in Mexico. GM CROPS & FOOD 2018; 9:152-168. [PMID: 30388927 PMCID: PMC6277063 DOI: 10.1080/21645698.2018.1507601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 07/11/2018] [Accepted: 07/26/2018] [Indexed: 11/03/2022]
Abstract
Mexico is a center of origin for several economically important plants including maize, cotton, and cocoa. Maize represents more than a food crop, has been declared a biological, cultural, agricultural and economic patrimony, and is linked to the national identity of Mexicans. In this review, we describe the historic and current use of genetically modified plants in Mexico and factors that contributed to the development of the biosafety regulation. We developed a database containing all permit applications received by the government to release genetically modified plants. A temporal and geographical analysis identified the plant species that have been authorized for experimental purposes, pilot programs, or commercial production, the geographic areas where they have been released, and the traits that have been introduced. Results show that Mexico has faced a dual challenge: accepting the benefits of genetically modified plants and their products, while protecting native plant biodiversity.
Collapse
Affiliation(s)
| | - Aaron N. Knapp
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, NE, USA
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, NE, USA
| |
Collapse
|
27
|
Long L, Guo DD, Gao W, Yang WW, Hou LP, Ma XN, Miao YC, Botella JR, Song CP. Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression. PLANT METHODS 2018; 14:85. [PMID: 30305839 PMCID: PMC6169012 DOI: 10.1186/s13007-018-0353-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND When developing CRISPR/Cas9 systems for crops, it is crucial to invest time characterizing the genome editing efficiency of the CRISPR/Cas9 cassettes, especially if the transformation system is difficult or time-consuming. Cotton is an important crop for the production of fiber, oil, and biofuel. However, the cotton stable transformation is usually performed using Agrobacterium tumefaciens taking between 8 and 12 months to generate T0 plants. Furthermore, cotton is a heterotetraploid and targeted mutagenesis is considered to be difficult as many genes are duplicated in this complex genome. The application of CRISPR/Cas9 in cotton is severely hampered by the long and technically challenging genetic transformation process, making it imperative to maximize its efficiency. RESULTS In this study, we provide a new system to evaluate and validate the efficiency of CRISPR/Cas9 cassettes in cotton using a transient expression system. By using this system, we could select the most effective CRISPR/Cas9 cassettes before the stable transformation. We have also optimized the existing cotton CRISPR/Cas9 system to achieve vastly improved mutagenesis efficiency by incorporating an endogenous GhU6 promoter that increases sgRNA expression levels over the Arabidopsis AtU6-29 promoter. The 300 bp GhU6.3 promoter was cloned and validated using the transient expression system. When sgRNAs were expressed under the control of the GhU6.3 promoter in CRISPR/Cas9 cassettes, expression levels were 6-7 times higher than those provided by the AtU6-29 promoter and CRISPR/Cas9-mediated mutation efficiency was improved 4-6 times. CONCLUSIONS This study provides essential improvements to maximize CRISPR/Cas9-mediated mutation efficiency by reducing risk and workload for the application of CRISPR/Cas9 approaches in the targeted mutagenesis of cotton.
Collapse
Affiliation(s)
- Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Dan-Dan Guo
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Wen-Wen Yang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Li-Pan Hou
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Yu-Chen Miao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Jose Ramon Botella
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| |
Collapse
|
28
|
Hahn F, Eisenhut M, Mantegazza O, Weber APM. Homology-Directed Repair of a Defective Glabrous Gene in Arabidopsis With Cas9-Based Gene Targeting. FRONTIERS IN PLANT SCIENCE 2018; 9:424. [PMID: 29675030 PMCID: PMC5895730 DOI: 10.3389/fpls.2018.00424] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/16/2018] [Indexed: 05/18/2023]
Abstract
The CRISPR/Cas9 system has emerged as a powerful tool for targeted genome editing in plants and beyond. Double-strand breaks induced by the Cas9 enzyme are repaired by the cell's own repair machinery either by the non-homologous end joining pathway or by homologous recombination (HR). While the first repair mechanism results in random mutations at the double-strand break site, HR uses the genetic information from a highly homologous repair template as blueprint for repair of the break. By offering an artificial repair template, this pathway can be exploited to introduce specific changes at a site of choice in the genome. However, frequencies of double-strand break repair by HR are very low. In this study, we compared two methods that have been reported to enhance frequencies of HR in plants. The first method boosts the repair template availability through the formation of viral replicons, the second method makes use of an in planta gene targeting (IPGT) approach. Additionally, we comparatively applied a nickase instead of a nuclease for target strand priming. To allow easy, visual detection of HR events, we aimed at restoring trichome formation in a glabrous Arabidopsis mutant by repairing a defective glabrous1 gene. Using this efficient visual marker, we were able to regenerate plants repaired by HR at frequencies of 0.12% using the IPGT approach, while both approaches using viral replicons did not yield any trichome-bearing plants.
Collapse
|
29
|
Jeon S, Lim JM, Lee HG, Shin SE, Kang NK, Park YI, Oh HM, Jeong WJ, Jeong BR, Chang YK. Current status and perspectives of genome editing technology for microalgae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:267. [PMID: 29163669 PMCID: PMC5686953 DOI: 10.1186/s13068-017-0957-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.
Collapse
Affiliation(s)
- Seungjib Jeon
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sung-Eun Shin
- LG Chem, 188 Munji-ro, Yuseong-gu, Daejeon, 34122 Republic of Korea
| | - Nam Kyu Kang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Byeong-ryool Jeong
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Keun Chang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| |
Collapse
|
30
|
Arora L, Narula A. Gene Editing and Crop Improvement Using CRISPR-Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1932. [PMID: 29167680 PMCID: PMC5682324 DOI: 10.3389/fpls.2017.01932] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/25/2017] [Indexed: 05/04/2023]
Abstract
Advancements in Genome editing technologies have revolutionized the fields of functional genomics and crop improvement. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat)-Cas9 is a multipurpose technology for genetic engineering that relies on the complementarity of the guideRNA (gRNA) to a specific sequence and the Cas9 endonuclease activity. It has broadened the agricultural research area, bringing in new opportunities to develop novel plant varieties with deletion of detrimental traits or addition of significant characters. This RNA guided genome editing technology is turning out to be a groundbreaking innovation in distinct branches of plant biology. CRISPR technology is constantly advancing including options for various genetic manipulations like generating knockouts; making precise modifications, multiplex genome engineering, and activation and repression of target genes. The review highlights the progression throughout the CRISPR legacy. We have studied the rapid evolution of CRISPR/Cas9 tools with myriad functionalities, capabilities, and specialized applications. Among varied diligences, plant nutritional improvement, enhancement of plant disease resistance and production of drought tolerant plants are reviewed. The review also includes some information on traditional delivery methods of Cas9-gRNA complexes into plant cells and incorporates the advent of CRISPR ribonucleoproteins (RNPs) that came up as a solution to various limitations that prevailed with plasmid-based CRISPR system.
Collapse
Affiliation(s)
| | - Alka Narula
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi, India
| |
Collapse
|
31
|
Murovec J, Pirc Ž, Yang B. New variants of CRISPR RNA-guided genome editing enzymes. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:917-926. [PMID: 28371222 PMCID: PMC5506654 DOI: 10.1111/pbi.12736] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 05/14/2023]
Abstract
CRISPR-mediated genome editing using the Streptococcus pyogenes Cas9 enzyme is revolutionizing life science by providing new, precise, facile and high-throughput tools for genetic modification by the specific targeting of double-strand breaks in the genome of hosts. Plant biotechnologists have extensively used the S. pyogenes Cas9-based system since its inception in 2013. However, there are still some limitations to its even broader usage in plants. Major restrictions, especially in agricultural biotechnology, are the currently unclear regulatory status of plants modified with CRISPR/Cas9 and the lack of suitable delivery methods for some plant species. Solutions to these limitations could come in the form of new variants of genome editing enzymes that have recently been discovered and have already proved comparable to or even better in performance than S. pyogenes CRISPR/Cas9 in terms of precision and ease of delivery in mammal cells. Although some of them have already been tested in plants, most of them are less well known in the plant science community. In this review, we describe the following new enzyme systems engineered for genome editing, transcriptional regulation and cellular imaging-C2c2 from L. shahii; Cas9 from F. novicida, S. aureus, S. thermophiles, N. meningitidis; Cpf1 from F. novicida, Acidaminococcus and Lachnospiraceae; nickase, split, enhanced and other Cas9 variants from S. pyogenes; catalytically inactive SpCas9 linked to various nuclease or gene-regulating domains-with an emphasis on their advantages in comparison with the broadly used SpCas9. In addition, we discuss new possibilities they offer in plant biotechnology.
Collapse
Affiliation(s)
- Jana Murovec
- Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Žan Pirc
- Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Bing Yang
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| |
Collapse
|
32
|
Odipio J, Alicai T, Ingelbrecht I, Nusinow DA, Bart R, Taylor NJ. Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava. FRONTIERS IN PLANT SCIENCE 2017; 8:1780. [PMID: 29093724 PMCID: PMC5651273 DOI: 10.3389/fpls.2017.01780] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/30/2017] [Indexed: 05/17/2023]
Abstract
CRISPR/Cas9 has become a powerful genome-editing tool for introducing genetic changes into crop species. In order to develop capacity for CRISPR/Cas9 technology in the tropical staple cassava (Manihot esculenta), the Phytoene desaturase (MePDS) gene was targeted in two cultivars using constructs carrying gRNAs targeting two sequences within MePDS exon 13. After Agrobacterium-mediated delivery of CRISPR/Cas9 reagents into cassava cells, both constructs induced visible albino phenotypes within cotyledon-stage somatic embryos regenerating on selection medium and the plants regenerated therefrom. A total of 58 (cv. 60444) and 25 (cv. TME 204) plant lines were recovered, of which 38 plant lines (19 from each cultivar) were analyzed for mutagenesis. The frequency of plant lines showing albino phenotype was high, ranging from 90 to 100% in cv. TME 204. Observed albino phenotypes were comprised of full albinos devoid of green tissue and chimeras containing a mixture of white and green tissues. Sequence analysis revealed that 38/38 (100%) of the plant lines examined carried mutations at the targeted MePDS site, with insertions, deletions, and substitutions recorded. One putatively mono-allelic homozygous line (1/19) was found from cv. 60444, while 1 (1/19) and 4 (4/19) putatively bi-allelic homozygous lines were found in 60444 and TME204, respectively. The remaining plant lines, comprised mostly of the chimeras, were found to be putatively heterozygous. We observed minor (1 bp) nucleotide substitutions and or deletions upstream of the 5' and or downstream of the 3' targeted MePDS region. The data reported demonstrates that CRISPR/Cas9-mediated genome editing of cassava is highly efficient and relatively simple, generating multi-allelic mutations in both cultivars studied. Modification of MePDS described here generates visually detectable mutated events in a relatively short time frame of 6-8 weeks, and does not require sequencing to confirm editing at the target. It therefore provides a valuable platform to facilitate rapid assessment and optimization of CRISPR/Cas9 and other genome-editing technologies in cassava.
Collapse
Affiliation(s)
- John Odipio
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- National Crops Resources Research Institute, Kampala, Uganda
- Vlaams Instituut voor Biotechnologie, Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - Ivan Ingelbrecht
- Vlaams Instituut voor Biotechnologie, Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | | | - Rebecca Bart
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Nigel J. Taylor
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- *Correspondence: Nigel J. Taylor,
| |
Collapse
|
33
|
Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 DOI: 10.3389/fpls.2017.01364/bibtex] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/20/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
Collapse
Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| |
Collapse
|
34
|
Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 PMCID: PMC5541054 DOI: 10.3389/fpls.2017.01364] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/17/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
Collapse
Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K. Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
- *Correspondence: Chunpeng Song,
| |
Collapse
|
35
|
Odipio J, Alicai T, Ingelbrecht I, Nusinow DA, Bart R, Taylor NJ. Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava. FRONTIERS IN PLANT SCIENCE 2017; 8:1780. [PMID: 29093724 DOI: 10.3389/fpls.2017.01780/bibte] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/30/2017] [Indexed: 05/20/2023]
Abstract
CRISPR/Cas9 has become a powerful genome-editing tool for introducing genetic changes into crop species. In order to develop capacity for CRISPR/Cas9 technology in the tropical staple cassava (Manihot esculenta), the Phytoene desaturase (MePDS) gene was targeted in two cultivars using constructs carrying gRNAs targeting two sequences within MePDS exon 13. After Agrobacterium-mediated delivery of CRISPR/Cas9 reagents into cassava cells, both constructs induced visible albino phenotypes within cotyledon-stage somatic embryos regenerating on selection medium and the plants regenerated therefrom. A total of 58 (cv. 60444) and 25 (cv. TME 204) plant lines were recovered, of which 38 plant lines (19 from each cultivar) were analyzed for mutagenesis. The frequency of plant lines showing albino phenotype was high, ranging from 90 to 100% in cv. TME 204. Observed albino phenotypes were comprised of full albinos devoid of green tissue and chimeras containing a mixture of white and green tissues. Sequence analysis revealed that 38/38 (100%) of the plant lines examined carried mutations at the targeted MePDS site, with insertions, deletions, and substitutions recorded. One putatively mono-allelic homozygous line (1/19) was found from cv. 60444, while 1 (1/19) and 4 (4/19) putatively bi-allelic homozygous lines were found in 60444 and TME204, respectively. The remaining plant lines, comprised mostly of the chimeras, were found to be putatively heterozygous. We observed minor (1 bp) nucleotide substitutions and or deletions upstream of the 5' and or downstream of the 3' targeted MePDS region. The data reported demonstrates that CRISPR/Cas9-mediated genome editing of cassava is highly efficient and relatively simple, generating multi-allelic mutations in both cultivars studied. Modification of MePDS described here generates visually detectable mutated events in a relatively short time frame of 6-8 weeks, and does not require sequencing to confirm editing at the target. It therefore provides a valuable platform to facilitate rapid assessment and optimization of CRISPR/Cas9 and other genome-editing technologies in cassava.
Collapse
Affiliation(s)
- John Odipio
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- National Crops Resources Research Institute, Kampala, Uganda
- Vlaams Instituut voor Biotechnologie, Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - Ivan Ingelbrecht
- Vlaams Instituut voor Biotechnologie, Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Dmitri A Nusinow
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Rebecca Bart
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| |
Collapse
|