Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana

Tripathi, Leena; Ntui, Valentine Otang; Tripathi, Jaindra Nath; Kumar, P. Lava

doi:10.3389/fmicb.2020.609784

Cited by 44 publications

(23 citation statements)

References 95 publications

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“…The accuracy and specificity of the CRISPR-Cas method in human virus diagnostics ( Chen et al, 2018 ; Curti et al, 2020 ) support its application as a reliable tool for plant virus diagnosis. The importance of CRISPR-Cas-based diagnostics assays in phytosanitary efforts to produce clean plant materials as part of surveillance programs has been elaborated for virus diagnosis in banana ( Tripathi et al, 2021 ). In this study, we have developed a CRISPR-Cas12a-based method for BNYVV detection in sugarbeet roots applicable for rhizomania diagnosis.…”

Section: Discussionmentioning

confidence: 99%

CRISPR-Based Isothermal Next-Generation Diagnostic Method for Virus Detection in Sugarbeet

2021

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Rhizomania is a disease of sugarbeet caused by beet necrotic yellow vein virus (BNYVV) that significantly affects sugarbeet yield globally. Accurate and sensitive detection methods for BNYVV in plants and field soil are necessary for growers to make informed decisions on variety selection to manage this disease. A recently developed CRISPR-Cas-based detection method has proven highly sensitive and accurate in human virus diagnostics. Here, we report the development of a CRISPR-Cas12a-based method for detecting BNYVV in the roots of sugarbeet. A critical aspect of this technique is the identification of conditions for isothermal amplification of viral fragments. Toward this end, we have developed a reverse transcription (RT) recombinase polymerase amplification (RPA) for detecting BNYVV in sugarbeet roots. The RT-RPA product was visualized, and its sequence was confirmed. Subsequently, we designed and validated the cutting efficiency of guide RNA targeting BNYVV via in vitro activity assay in the presence of Cas12a. The sensitivity of CRISPR-Cas12a trans reporter-based detection for BNYVV was determined using a serially diluted synthetic BNYVV target sequence. Further, we have validated the developed CRISPR-Cas12a assay for detecting BNYVV in the root-tissue of sugarbeet bait plants reared in BNYVV-infested field soil. The results revealed that BNYVV detection is highly sensitive and specific to the infected roots relative to healthy control roots as measured quantitatively through the reporter signal. To our knowledge, this is the first report establishing isothermal RT-RPA- and CRISPR-based methods for virus diagnostic approaches for detecting BNYVV from rhizomania diseased sugarbeet roots.

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Section: Discussionmentioning

confidence: 99%

CRISPR-Based Isothermal Next-Generation Diagnostic Method for Virus Detection in Sugarbeet

2021

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“…Currently, many countries do not have a clear regulatory framework for GE crops. However, several countries like Kenya, Nigeria, and India are in the process of developing the regulatory guidelines for the application of genome editing [77].…”

Section: Regulations On Genome Edited Cropsmentioning

confidence: 99%

Prospects for Genome Editing of Potato

Dev¹,

Joseph²,

D’Rosario³

2021

Solanum Tuberosum - A Promising Crop for Starvation Problem

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Potato (Solanum tuberosum L.) is a staple food crop that could play a major role in improving food security in developing nations. The sustainable production of this crop faces many challenges like pests, diseases, abiotic stresses and post-harvest problems. Transgenic technology and gene silencing strategies offered a new hope of solution to the conventional time consuming breeding programmes. However the genetically modified crops are affected by regulatory approvals and safety concerns. In this aspect, gene editing techniques like ZFNs (zinc-finger nucleases), TALENs (transcription activator-like effector nucleases), and CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated Cas9), offer better choice for production of transgene and marker free disease resistant potatoes.

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“…Genome editing of first fruit and berry cultures has been conducted by CRISPR/Cas9 fairly recent [23][24][25]. This review summarizes the results of CRISPR/Cas9 genome editing studies of different groups of target genes in fruit and berry crops: (1) in order to decrease biotic and abiotic stress susceptibility [19,[24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39], (2) change flowering time and plant architectonics [40][41][42][43][44][45], (3) increase shelf-time [46], (4) study gene functions [43][44][45][47][48][49] and (5) optimize CRISPR/Cas9 editing of fruit and berry cultures by using the marker [22,23,32,41,43,44,[50][51][52][53][54][55][56][57]…”

Section: Introductionmentioning

confidence: 99%

Applications of CRISPR/Cas9 System in Vegetatively Propagated Fruit and Berry Crops

et al. 2021

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Fruit and berry crops, as well as grapes, are important parts of the human diet and, at the same time, significant objects of genetic, breeding, biochemical and nutritional research. Traditional approaches of crop research and improvement are now complemented by effective modern genetic technologies. In this review, we analyze and summarize the achievements in genome editing of fruit, berry crops and grapes. New approaches accelerate the improvement of genotypes for many groups of traits: plant resistance to unfavorable environmental factors, flowering and ripening time, plant architectonics, fruit shelf time and biochemical composition. Genome editing using the CRISPR/Cas9 system has been successfully tested on the most important vegetatively propagated fruit and berry crops (apple, pear, orange, kumquat, grapefruit, banana, strawberry and kiwi) and grapes. About 30 genes of these crops have been used as targets for the introduction of desired mutations using the CRISPR/Cas9 system. The most valuable results are the improvement of important agronomic traits. For 24 genes it has been shown that their knockout can result in the improvement of varieties. In addition, the review pays attention to the comparative analysis of the explant types of vegetatively propagated crops used for the delivery of editing genetic constructs, as well as the comparison of the editing efficiency depending on the variation of the objects used, delivery methods, etc. The article discusses the existing limitations that need to be overcome for a wider application of genomic editing in order to improve varieties of fruit and berry crops, as well as grapes.

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Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana

Cited by 44 publications

References 95 publications

CRISPR-Based Isothermal Next-Generation Diagnostic Method for Virus Detection in Sugarbeet

CRISPR-Based Isothermal Next-Generation Diagnostic Method for Virus Detection in Sugarbeet

Prospects for Genome Editing of Potato

Applications of CRISPR/Cas9 System in Vegetatively Propagated Fruit and Berry Crops

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