Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects

Singha, Dhanawantari L.; Das, Debajit; Sarki, Yogita N.; Chowdhury, Naimisha; Sharma, Monica; Maharana, Jitendra; Chikkaputtaiah, Channakeshavaiah

doi:10.1007/s00425-021-03811-0

Cited by 15 publications

(8 citation statements)

References 153 publications

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“…However, their mutation ratios are low, and the mutation sites are random and unknown. The CRISPR/Cas9 system can easily produce target gene mutation, and has been widely used in plant mutant creation, especially for reverse genetics in revealing target gene function and regulation [6][7][8][9][10]. The Cas9 protein functions as a nuclease and is guided to the target site by the engineered single guide RNA (gRNA) including 20 specific nucleotides of the selected gene to determine the site-specific targeting.…”

Section: Discussionmentioning

confidence: 99%

“…The reverse genetics can reveal the gene function through the mutation or expression regulation of target gene [1,2]. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system can easily mutate and edit the target gene, and has been widely used in plant sciences and crop improvement [6][7][8][9][10]. The mutants induced by CRISPR/Cas system usually have many heterozygous and bi-allelic mutant lines, which can produce the homozygous mutant plants in their offspring segregation population [11][12][13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

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Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice

Jiang

Ren

Wang

et al. 2022

Plants

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Bi-allelic mutant lines induced by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems are important genetic materials. It is very important to establish a rapid and cheap method in identifying homozygous mutant plants from offspring segregation populations of bi-allelic mutant lines. In this study, the offspring genotypes of rice bi-allelic starch branching enzyme IIb mutant lines were identified using the allele specific PCR (AS-PCR) method. The target sequences of two alleles were aligned from their 5′ to 3′ ends, and the first different bases were used as the 3′ ends of mismatch primers. Another mismatched base was introduced at the third nucleotide from the 3′ end of mismatch primer. The PCR reaction mixture and amplification program were optimized according to the differences of mutation target sequence and mismatch primers. The offspring plant genotypes of bi-allelic mutant lines could be accurately identified using the amplified DNA fragments by agarose gel electrophoresis. This study could provide a method reference for the rapid screening of homozygous mutant plants from offspring segregation population of heterozygous and bi-allelic mutant lines.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice

Jiang

Ren

Wang

et al. 2022

Plants

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“…ZFNs, mega-nucleases, TALENs, and CRISPR/Cas9 are famous gene editing tools which have been demonstrated for targeted gene modifications in plants (Aziz 2021). CRISPR is a well-known bacterial immune defense system with it's the best and well know tools known as CRISPR that laid the new foundation for biotechnologies on CRISPR-Cas9 (Singha et al 2022).…”

Section: Gened Tools Used For Targeted Genome Modificationsmentioning

confidence: 99%

Genome editing in cotton: challenges and opportunities

Khan

Ahmed

et al. 2023

J Cotton Res

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Cotton has enormous economic potential providing high-quality protein, oil, and fibre. A large increase in cotton output is necessary due to the world's changing climate and constantly expanding human population. In the past, conventional breeding techniques were used to introduce genes into superior cotton cultivars to increase production and to improve quality. The disadvantages of traditional breeding techniques are their time-consuming, reliance on genetic differences that are already present, and considerable backcrossing. To accomplish goals in a short amount of time, contemporary plant breeding techniques, in particular modern genome editing technologies (GETs), can be used. Numerous crop improvement initiatives have made use of GETs, such as zinc-finger nucleases, transcription-activator-like effector nucleases, clustered regularly interspaced palindromic repeats (CRISPR), and CRISPR-associated proteins systems (CRISPR/Cas)-based technologies. The CRISPR/Cas system has a lot of potential because it combines three qualities that other GETs lack: simplicity, competence, and adaptability. The CRISPR/Cas mechanism can be used to improve cotton tolerance to biotic and abiotic stresses, alter gene expression, and stack genes for critical features with little possibility of segregation. The transgene clean strategy improves CRISPR acceptability addressing regulatory issues associated with the genetically modified organisms (GMOs). The research opportunities for using the CRISPR/Cas system to address biotic and abiotic stresses, fibre quality, plant architecture and blooming, epigenetic changes, and gene stacking for commercially significant traits are highlighted in this article. Furthermore, challenges to use of CRISPR technology in cotton and its potential for the future are covered in detail.

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“…Tissue-specific genome editing can effectively reduce the activity of the off-targets in the palm, which is not efficiently predicted and confirmed by in-silico predictions. Readers may get more detailed information about tissue-specific genome editing in a recently published review ( Singha et al., 2022 ).…”

Section: Crispr-based Genome Editing Systems In Treesmentioning

confidence: 99%

Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits

et al. 2022

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Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms’ importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population’s demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.

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Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects

Cited by 15 publications

References 153 publications

Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice

Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice

Genome editing in cotton: challenges and opportunities

Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits

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