Guidelines for C to T base editing in plants: base-editing window, guide RNA length, and efficient promoter

Kang, Beum‐Chang; Woo, Je Wook; Bae, Su‐Ji; Choi, Myeon-Song; Kim, Jin‐Soo; Kim, Sang‐Gyu

doi:10.1007/s11816-019-00572-x

Cited by 7 publications

(5 citation statements)

References 27 publications

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“…In a base editing procedure, gRNAs should be designed such that the targeted base is located between positions 4 and 8 in the gRNA sequences (editing window), counting the end distal to the PAM as position 1 [89]. Two CBEs have been conducted in soybean, and their results showed that the editing window of nCas9-APOBEC1 is located between positions 5-7 in the gRNA sequence, counting the end distal to the PAM as position 1 [90,91].…”

Section: Chimeric Deactivated Cas9 Proteins and Their Applicationsmentioning

confidence: 99%

CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean

Niazian

Belzile

Torkamaneh

2022

Plants

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Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene’s function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective “in root” functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.

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Section: Chimeric Deactivated Cas9 Proteins and Their Applicationsmentioning

confidence: 99%

CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean

Niazian

Belzile

Torkamaneh

2022

Plants

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“…It is thus necessary to develop an optimal system for the controlled manipulation of SlJUL expression to revamp the phloem cell population and increase yield traits without compromising plant growth. To achieve this, promoter engineering and base editing using CRISPR‐Cas9 could be considered (Kang et al ., 2019 ; Kwon et al ., 2020 ; Mishra et al ., 2020 ; Rodríguez‐Leal et al ., 2017 ; Shimatani et al ., 2017 ), or tissue‐ or organ‐specific promoters could be used to drive JUL expression in a spatiotemporal manner without causing any pleiotropic effects on plant growth. However, a clear understanding of the probable correlation between crop productivity and the regulation of SlJUL expression and its activity in controlling the phloem cell population to varying degrees is still lacking and should be a subject for future studies.…”

Section: Discussionmentioning

confidence: 99%

JULGI‐mediated increment in phloem transport capacity relates to fruit yield in tomato

Nam

Gupta

Nam

et al. 2022

Plant Biotechnology Journal

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Summary The continuous growth of the global population and the increase in the amount of arid land has severely constrained agricultural crop production. To solve this problem, many researchers have attempted to increase productivity through the efficient distribution of energy; however, the direct relationship between the plant vasculature, specifically phloem development, and crop yield is not well established. Here, we demonstrate that an optimum increase in phloem‐transportation capacity by reducing SIJUL expression leads to improved sink strength in tomato (Solanum lycopersicum L.). SIJUL, a negative regulator of phloem development, suppresses the translation of a positive regulator of phloem development, SlSMXL5. The suppression of SlJUL increases the number of phloem cells and sucrose transport, but only an optimal reduction of SlJUL function greatly enhances sink strength in tomato, improving fruit setting, and yield contents by 37% and 60%, respectively. We show that the increment in phloem cell number confers spare transport capacity. Our results suggest that the control of phloem‐transport capacity within the threshold could enhance the commitment of photosynthates to instigate yield improvement.

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“…Fortunately, developing crop varieties harboring herbicide-resistant mutations that render crop tolerance to ALS-inhibiting herbicides by the CBE has been successfully applied in various crop species, including rice [61,95], maize [64], wheat [53,54], watermelon [55], oilseed rape [56], tobacco [57], tomato, and potato [58]. Similarly, crop tolerance to ACCaseinhibiting herbicides was also found in wheat via the CBE editor [53].…”

Section: Improving Herbicide Resistance Through Base Editingmentioning

confidence: 99%

The Development of Herbicide Resistance Crop Plants Using CRISPR/Cas9-Mediated Gene Editing

Dong

Huang

Wang

2021

Genes

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The rapid increase in herbicide-resistant weeds creates a huge challenge to global food security because it can reduce crop production, causing considerable losses. Combined with a lack of novel herbicides, cultivating herbicide-resistant crops becomes an effective strategy to control weeds because of reduced crop phytotoxicity, and it expands the herbicidal spectrum. Recently developed clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas)-mediated genome editing techniques enable efficiently targeted modification and hold great potential in creating desired plants with herbicide resistance. In the present review, we briefly summarize the mechanism responsible for herbicide resistance in plants and then discuss the applications of traditional mutagenesis and transgenic breeding in cultivating herbicide-resistant crops. We mainly emphasize the development and use of CRISPR/Cas technology in herbicide-resistant crop improvement. Finally, we discuss the future applications of the CRISPR/Cas system for developing herbicide-resistant crops.

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Guidelines for C to T base editing in plants: base-editing window, guide RNA length, and efficient promoter

Cited by 7 publications

References 27 publications

CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean

CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean

JULGI‐mediated increment in phloem transport capacity relates to fruit yield in tomato

The Development of Herbicide Resistance Crop Plants Using CRISPR/Cas9-Mediated Gene Editing

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