4.6 Review

Comprehending the evolution of gene editing platforms for crop trait improvement

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Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies

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Summary: Soybean, an important crop among legumes due to its high nutritional content, is used globally for food, feed, and fuel. Conventional breeding and new biotechnological methods have allowed for the improvement of soybean traits to fulfill consumer demands and address global food deficiency. New plant breeding technologies, such as CRISPR/Cas9, have enhanced the genetic modification of soybean and addressed ethical and public acceptance concerns. This review discusses the improvement of soybean through genetic engineering and NPBTs, highlighting valuable traits and potential targets for further improvement.

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Applications of CRISPR/Cas9 technology for modification of the plant genome

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Summary: The CRISPR/Cas system, originally a bacterial and archeal acquired immune response, has evolved into an efficient genome editing tool widely used in plant genetic engineering. It utilizes programmable sgRNAs to guide the Cas9 endonuclease to the target DNA location, resulting in the generation of plant varieties with desired traits such as disease resistance and nutritional enhancement.

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Deletion and replacement of long genomic sequences using prime editing

Tingting Jiang et al.

Summary: The study optimized prime editing tools for creating precise genomic deletions and direct replacement of a genomic fragment with a desired sequence without the need for an exogenous DNA template. By conjugating Cas9 nuclease to reverse transcriptase and using two PE guide RNAs targeting complementary DNA strands, the PEDAR method achieved precise and specific deletion and repair of target sequences.

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Yuan Zhuang et al.

Summary: The HOPE method utilizes paired pegRNAs encoding the same edits to achieve high editing efficiency in human embryonic kidney and colorectal carcinoma cells, showing improved product purity compared to the original PE3 system. This enhanced tool has the potential to broaden both fundamental research and therapeutic applications of prime editing.

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Strong and tunable anti-CRISPR/Cas activities in plants

Camilo Calvache et al.

Summary: This study demonstrates that anti-CRISPR proteins AcrIIA4 and AcrVA1 can prevent CRISPR/Cas-mediated gene editing in plants, opening up new possibilities for customized control of gene editing and gene expression.

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Classification of CRISPR/Cas system and its application in tomato breeding

Abira Chaudhuri et al.

Summary: This review provides a comprehensive overview of the different types of CRISPR systems in bacteria and archaea, and discusses the application of CRISPR/Cas9 in genome editing and tomato breeding.

THEORETICAL AND APPLIED GENETICS (2022)

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Modification of tomato breeding traits and plant hormone signaling by Target-AID, the genome-editing system inducing efficient nucleotide substitution

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Summary: Target-AID is a CRISPR/Cas9-based genome-editing tool that confers base-editing capability on the Cas9 system. In this study, we successfully applied the Target-AID system to edit negative regulators of the plant hormone signaling pathway in tomatoes, demonstrating its potential for molecular breeding in tomato crops.

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Use of CRISPR/Cas9-Based Gene Editing to Simultaneously Mutate Multiple Homologous Genes Required for Pollen Development and Male Fertility in Maize

Xinze Liu et al.

Summary: This study investigates the role of multiple homologous genes in anther and pollen development in maize. The researchers used the CRISPR/Cas9 gene editing system to simultaneously mutate homologs in several putative GMS gene families. They identified the functions of these genes in controlling maize male fertility and demonstrated the efficiency of the gene editing system in identifying multiple homologous GMS genes.
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AGBE: a dual deaminase-mediated base editor by fusing CGBE with ABE for creating a saturated mutant population with multiple editing patterns

Yanhui Liang et al.

Summary: Establishing saturated mutagenesis is an efficient method for studying the relationships between mutations and phenotypes. The AGBE system, which combines glycosylase base editor and ABE, allows the introduction of multiple base conversions and indels in mammalian cells.

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Expanding the plant genome editing toolbox with recently developed CRISPR-Cas systems

Naoki Wada et al.

Summary: Recently discovered and characterized CRISPR-Cas systems provide new tools for plant genome editing. Several new CRISPR-Cas systems have been applied successfully to plant and human genome editing, offering higher specificity and unique characteristics compared to known Cas proteins.

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Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato

Pierre-Francois Perroud et al.

Summary: The introduction of CRISPR-Cas9 technology has revolutionized plant research and precision crop breeding, while the development of Prime Editing technology has opened up new possibilities for precise genome editing in plants. Successful application of Prime Editing in Physcomitrium patens and potato demonstrated its unique advantage in introducing nucleotide substitutions, with high targeting fidelity observed in P. patens.

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Huanan Han et al.

Summary: Base editing using CRISPR technologies is a valuable tool for crop breeding. Researchers have developed a high-efficiency wheat ABE (WhieABE) tool, which increases wheat resistance to a widely used herbicide by mutating wheat tubulin alleles. This study promises to accelerate crop improvement and develop herbicide-resistant wheat germplasm.

CROP JOURNAL (2022)

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CRISPR-Cas genome editing system: A versatile tool for developing disease resistant crops

Ashwini Talakayala et al.

Summary: The productivity of crops is seriously threatened by phyto-pathogens, such as viruses, bacteria, and fungi, which cause significant crop loss worldwide. Developing disease-resistant crop varieties is crucial to meet the growing population's needs. The CRISPR/Cas9 genome editing tool has revolutionized plant research and has been extensively used to develop disease resistance in plants. By editing genes involved in the interaction with pathogens, crop plants such as rice, wheat, cucumber, cassava, cacao, grapes, citrus, apple, and banana have improved disease resistance. The applications and limitations of developing transgene-free disease resistant crops have also been discussed.

PLANT STRESS (2022)

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A design optimized prime editor with expanded scope and capability in plants

Wen Xu et al.

Summary: This study demonstrated that using N-terminal reverse transcriptase-Cas9 nickase fusion and introducing multiple-nucleotide substitutions in the reverse transcriptase template can significantly enhance the efficiency of prime editing in plants and human cells. The optimized approach achieved higher editing frequencies compared to the original editor, Prime Editor 3, showing the potential to make previously non-editable target sites editable and expand the capabilities of prime editing in the future.

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CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells

Ibrahim C. Kurt et al.

Summary: This study presents two base editor architectures that can efficiently induce targeted C-to-G base transversions, with reduced levels of unwanted mutations. These new base editors hold promise for optimizing C-to-G base editors for both research and therapeutic applications.

NATURE BIOTECHNOLOGY (2021)

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Dongdong Zhao et al.

Summary: The study introduces novel glycosylase base editors (GBEs) that can induce C-to-A and C-to-G transversions in Escherichia coli and mammalian cells, respectively. The new editors exhibit high editing specificity and efficiency, making them potential tools for targeting G/C disease-causing mutations.

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Yang Xu et al.

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Base editing with high efficiency in allotetraploid oilseed rape by A3A-PBE system

Hongtao Cheng et al.

Summary: The study established an A3A-PBE base-editing system in allotetraploid Brassica napus, demonstrating high editing efficiency and broadened editing window. Mutants for ALS, IAA7, and RGA genes showed different traits, with potential applications in herbicide resistance or plant architecture improvement. Target sequencing identified an editing window from C1 to C10 and confirmed base-editing inheritance from T(0) to T(1) generations with several Indel mutations at target sites.

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Epigenetics for Crop Improvement in Times of Global Change

Ioanna Kakoulidou et al.

Summary: Research on plant epigenetics aims to understand how various factors regulate plant development independently of genome changes. Epigenetic changes can be heritable and impact plant growth and crop tolerance, particularly in response to environmental stimuli. Harnessing epigenetic diversity can lead to engineered plants with advantageous traits for optimal crop production.

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Jaiana Malabarba et al.

Summary: Despite obstacles, progress has been made in using CRISPR/Cas9 in perennial plants. A regeneration step can reduce initial chimerism and enable accurate genome edits. Base editing tools have been successfully applied in apple and pear to induce precise DNA substitutions and generate new alleles.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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CRISPR technologies for precise epigenome editing

Muneaki Nakamura et al.

Summary: The review discusses CRISPR-based epigenome engineering technologies for modulating histone and DNA modifications, perturbing DNA and RNA regulatory elements, and chromatin organization. The epigenome involves complex cellular processes governing genomic activity. Repurposing prokaryotic CRISPR systems has enabled the development of diverse technologies in epigenome engineering.

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Editing miR482b and miR482c Simultaneously by CRISPR/Cas9 Enhanced Tomato Resistance to Phytophthora infestans

Yuhui Hong et al.

Summary: The study successfully knocked out miR482b and miR482c simultaneously in tomatoes using the CRISPR/Cas9 system, resulting in transgenic plants with increased resistance to late blight. Simultaneous knockout of miR482b and miR482c was more effective than knocking out miR482b alone, and led to perturbations in the expression of other miRNAs.

PHYTOPATHOLOGY (2021)

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CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato

Ilan Ben Shlush et al.

Summary: Homologous recombination in somatic cells can be achieved through targeted induction of DNA double-strand breaks, resulting in restoration of gene activity and visualization as red phenotypes. The study found that some potential recombination events were caused by the appearance of red sectors on tangerine fruits.
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Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins

Liwei Chen et al.

Summary: A new class of base editors, C:G to G:C Base Editors, have been developed in this study to create single-base genomic transversions in human cells, targeting specific genes related to genetic diseases. These editors predominantly perform C:G to G:C editing with high purity and efficiency, showing therapeutic potential for interrogating and correcting human genetic diseases.

NATURE COMMUNICATIONS (2021)

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Genome Editing of Rice eIF4G Loci Confers Partial Resistance to Rice Black-Streaked Dwarf Virus

Wei Wang et al.

Summary: This study successfully generated eIF4G mutants with partial resistance to rice black-streaked dwarf virus (RBSDV) through CRISPR/Cas9 technology, which exhibited enhanced tolerance to virus infection. However, the mutants showed the same sensitivity to rice stripe virus (RSV) infection as wild-type plants, indicating specificity in resistance mechanisms against different viruses. Additionally, the eIF4G mutants had reduced eIF4G transcript levels and interacted directly with RBSDV, highlighting their potential as disease-resistant resources for developing RBSDV-resistant varieties.

VIRUSES-BASEL (2021)

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CRISPR-Cas technology based genome editing for modification of salinity stress tolerance responses in rice (Oryza sativa L.)

Ibrahim Khan et al.

Summary: CRISPR-Cas technology is effective in enhancing salt tolerance in rice through precise gene editing. 51 rice genes crucial for response to salinity stress have been identified. Issues such as off-target effects of CRISPR-Cas technology and their solutions have been highlighted.

MOLECULAR BIOLOGY REPORTS (2021)

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Novel and emerging biotechnological crop protection approaches

Gaetano Giudice et al.

Summary: This review focuses on challenging biotechnological approaches for breeding crops tolerant to biotic and abiotic stresses, as well as new techniques based on RNA interference and epigenome modifications to improve plant resilience. Recent advances in these applications are mainly reported for non-model plants and woody crops, and their combination with traditional breeding is discussed as a potential contribution to modern agriculture and climate change mitigation.

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Highly efficient C-to-T and A-to-G base editing in a Populus hybrid

Gen Li et al.

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Minkyung Choi et al.

Summary: CRISPR/Cas9-mediated genome editing is a crucial technology in modern biological research, and recent advancements in base-editing CRISPR tools have enabled targeted nucleotide substitutions. This study demonstrates the efficiency of cytosine base editors in Arabidopsis thaliana and highlights the impact of promoter choice on base-editing efficiencies in plants. The findings provide a strategy to optimize low-efficiency base editors and showcase their applicability for functional assays and trait development in crop research.

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ABE8e with Polycistronic tRNA-gRNA Expression Cassette Sig-Nificantly Improves Adenine Base Editing Efficiency in Nicotiana benthamiana

Zupeng Wang et al.

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INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Development of an efficient plant dual cytosine and adenine editor

Rongfang Xu et al.

Summary: The research team developed eCDAL and pDuBE1 to achieve high editing efficiency in plant cells, providing powerful tools for precise editing of plant genomes.

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High-efficiency plastome base editing in rice with TAL cytosine deaminase

Riqing Li et al.

MOLECULAR PLANT (2021)

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CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase

Basudev Ghoshal et al.

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Simon Sretenovic et al.

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Lei Liu et al.

Summary: By using CRISPR-Cas9 genome editing, weak promoter alleles of CLE genes and a null allele of a partially redundant compensating CLE gene were engineered in maize to increase multiple maize grain-yield-related traits, demonstrating the potential of genomic editing in crop improvement.

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Dongdong Zhao et al.

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Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus

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MOLECULAR PLANT (2016)

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MOLECULAR THERAPY (2016)

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NATURE (2016)

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NATURE REVIEWS MICROBIOLOGY (2016)

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SCIENTIFIC REPORTS (2016)

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SCIENTIFIC REPORTS (2016)

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MOLECULAR CELL (2015)

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In vivo genome editing using Staphylococcus aureus Cas9

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NATURE (2015)

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Benjamin P. Kleinstiver et al.

NATURE BIOTECHNOLOGY (2015)

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NATURE REVIEWS MICROBIOLOGY (2015)

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Editorial Material Multidisciplinary Sciences

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Caixia Gao

NATIONAL SCIENCE REVIEW (2015)

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High-frequency, precise modification of the tomato genome

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GENOME BIOLOGY (2015)

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SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

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NATURE (2014)

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NATURE (2014)

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Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

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NATURE BIOTECHNOLOGY (2014)

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Fusion of catalytically inactive Cas9 to Fokl nuclease improves the specificity of genome modification

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Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity

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NATURE COMMUNICATIONS (2014)

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Site-Specific Gene Targeting Using Transcription Activator-Like Effector (TALE)-Based Nuclease in Brassica oleracea

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JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2013)

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SCIENCE (2013)

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NATURE BIOTECHNOLOGY (2012)

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SCIENCE (2012)

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NATURE COMMUNICATIONS (2012)

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Review Plant Sciences

Xanthomonas AvrBs3 Family-Type III Effectors: Discovery and Function

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ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 48 (2010)

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The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

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MOLECULAR CELL (2010)

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Precise genome modification in the crop species Zea mays using zinc-finger nucleases

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NATURE (2009)

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CRISPR provides acquired resistance against viruses in prokaryotes

Rodolphe Barrangou et al.

SCIENCE (2007)

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Targeted mutagenesis using zinc-finger nucleases in Arabidopsis

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)