Conferring DNA virus resistance with high specificity in plants using virus-inducible genome-editing system

Ji, Xiang; Si, Xiaomin; Zhang, Yi; Zhang, Huawei; Zhang, Feng; Gao, Caixia

doi:10.1186/s13059-018-1580-4

Cited by 63 publications

(35 citation statements)

References 34 publications

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“…Three hundred and twenty six out of 468 studies were rated high validity, 44 to have medium/high and medium/low validity, 72 to have low validity, and 26 to have unclear validity. One study potentially rated as high validity was downgraded to low validity because the sgRNA/Cas9 complex was constitutively overexpressed but it is not traceable how this overexpression was actually achieved (Ji et al, 2018). Detailed information about the validity assessment of all studies including the reason for their classification is provided in Table 5 and Supplementary Table 5.…”

Section: Results Critical Appraisalmentioning

confidence: 99%

Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants

et al. 2020

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CRISPR/Cas enables a targeted modification of DNA sequences. Despite their ease and efficient use, one limitation is the potential occurrence of associated off-target effects. This systematic review aims to answer the following research question: Which factors affect the occurrence of off-target effects caused by the use of CRISPR/Cas in plants? Literature published until March 2019 was considered for this review. Articles were screened for relevance based on pre-defined inclusion criteria. Relevant studies were subject to critical appraisal. All studies included in the systematic review were synthesized in a narrative report, but studies rated as high and medium/high validity were reported separately from studies rated as low and medium/low or unclear validity. In addition, we ran a binary logistic regression analysis to verify five factors that may affect the occurrence of off-target effects: (1) Number of mismatches (2) Position of mismatches (3) GC-content of the targeting sequence (4) Altered nuclease variants (5) Delivery methods. In total, 180 relevant articles were included in this review containing 468 studies therein. Seventy nine percentage of these studies were rated as having high or medium/high validity. Within these studies, 6,416 potential off-target sequences were assessed for the occurrence of off-target effects. Results clearly indicate that an increased number of mismatches between the on-target and potential off-target sequence steeply decreases the likelihood of off-target effects. The observed rate of off-target effects decreased from 59% when there is one mismatch between the on-target and off-target sequences toward 0% when four or more mismatches exist. In addition, mismatch/es located within the first eight nucleotides proximal to the PAM significantly decreased the occurrence of off-target effects. There is no evidence that the GC-content significantly affects off-target effects. The database regarding the impact of the nuclease variant and the delivery method is very poor as the majority of studies applied the standard nuclease SpCas9 and the CRISPR/Cas system was stably delivered in the genome. Hence, a general significant impact of these two factors on the occurrence of off-target effects cannot be proved. This identified evidence gap needs to be filled by systematic studies exploring these individual factors in sufficient numbers.

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Section: Results Critical Appraisalmentioning

confidence: 99%

Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants

et al. 2020

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“…Geminiviral-based DNA replicons of wheat was utilized for transient expression of the CRISPR/Cas9 system against wheat dwarf virus ( WDV ), in hexaploid wheat and 12 fold upregulation was observed in ubiquitin gene expression [210]. Stable over-expression of sgRNAs and Cas9 that particularly target the genome of the Gemini-virus to prevent its growth has been applied for virus-resistant crop breeding programs [211,212,213]. Furthermore, the CRISPR/Cas9 system can also be used to mutate viral genomes in addition to tackling diseases caused by them [201].…”

Section: Applications Of Crispr/cas9 In Plant Breedingmentioning

confidence: 99%

“…Furthermore, the CRISPR/Cas9 system can also be used to mutate viral genomes in addition to tackling diseases caused by them [201]. The efficiency of CRISPR/Cas9-mediated viral GE can be increased by using virus promoters to govern sgRNA/Cas9 expression cassettes [211]. Recently, a new ortholog of Cas9 has been discovered in Francisella novicida (FnCas9) to edit RNA virus genomes.…”

Section: Applications Of Crispr/cas9 In Plant Breedingmentioning

confidence: 99%

Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox

Razzaq

Saleem

Kanwal

et al. 2019

IJMS

145

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Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.

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“…For example, the CRISPR/Cas9 system based on DNA viruses (BeYDV, WDV, and cabbage leaf curl virus) and RNA viruses (TRV, PEBV, TMV, beet necrotic yellow vein virus, and barley stripe mosaic virus) have demonstrated efficient gene targeting frequencies in model plants (N. benthamiana and A. thaliana) and crops (potato, tomato, rice, wheat, and maize) (Cody et al, 2017;Zaidi and Mansoor, 2017;Hameed et al, 2018;Hu et al, 2019;Jiang et al, 2019). In order to decrease the off-target effects of antiviral strategies mediated by the CRISPR/Cas9 system in plants, (Ji et al, 2018) developed two virus-induced gene editing vectors, in which the pV86 and pC86 promoters of BSCTV were trans-activated by co-infecting BSCTV. These BSCTV-inducible vectors were spatially and temporally responsive and inhibited BSCTV accumulation in both transient (N. benthamiana) and transgenic (A. thaliana) assays without off-target defect.…”

Section: The Promising Host Susceptibility Genes For Antiviral Enginementioning

confidence: 99%

Control of Plant Viruses by CRISPR/Cas System-Mediated Adaptive Immunity

Cao

Zhou

et al. 2020

Front. Microbiol.

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Plant diseases caused by invading plant viruses pose serious threats to agricultural production in the world, and the antiviral engineering initiated by molecular biotechnology has been an effective strategy to prevent and control plant viruses. Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system-mediated DNA or RNA editing/interference in plants make them very attractive tools applicable to the plant protection field. Here, we review the development of CRISPR/Cas systems and summarize their applications in controlling different plant viruses by targeting viral sequences or host susceptibility genes. We list some potential recessive resistance genes that can be utilized in antiviral breeding and emphasize the importance and promise of recessive resistance gene-based antiviral breeding to generate transgene-free plants without developmental defects. Finally, we discuss the challenges and opportunities for the application of CRISPR/Cas techniques in the prevention and control of plant viruses in the field.

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Conferring DNA virus resistance with high specificity in plants using virus-inducible genome-editing system

Cited by 63 publications

References 34 publications

Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants

Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants

Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox

Control of Plant Viruses by CRISPR/Cas System-Mediated Adaptive Immunity

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