scholarly journals Mutation Breeding in Tomato: Advances, Applicability and Challenges

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 128 ◽  
Author(s):  
Juhi Chaudhary ◽  
Alisha Alisha ◽  
Vacha Bhatt ◽  
Sonali Chandanshive ◽  
Nirbhay Kumar ◽  
...  
Keyword(s):  
Genome Editing ◽  
Large Scale ◽  
Insertional Mutagenesis ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Tomato Crop ◽  
Technological Advances ◽  
Trait Improvement ◽  
Induced Mutagenesis ◽  
Efficient Exploration

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

scholarly journals CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 797
Author(s):  
Muntazir Mushtaq ◽  
Aejaz Ahmad Dar ◽  
Milan Skalicky ◽  
Anshika Tyagi ◽  
Nancy Bhagat ◽  
...  
Keyword(s):  
Genome Editing ◽  
Crop Improvement ◽  
Fine Tuning ◽  
Plant Genome ◽  
Base Editing ◽  
Global Food Security ◽  
Technological Advances ◽  
Efficient Delivery ◽  
Future Challenges ◽  
Recent Developments

Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.

scholarly journals Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

2021 ◽  
Vol 22 (2) ◽  
pp. 682
Author(s):  
Hymavathi Salava ◽  
Sravankumar Thula ◽  
Vijee Mohan ◽  
Rahul Kumar ◽  
Fatemeh Maghuly
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Genome Editing ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Nutritional Quality ◽  
Insertional Mutagenesis ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Crop Plants

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.

scholarly journals Current and Future Prospects of Plant Breeding with CRISPR/Cas

2019 ◽  
pp. 1-17
Author(s):  
Wagh Sopan Ganpatrao ◽  
Pohare Manoj Baliram
Keyword(s):  
Plant Breeding ◽  
Genome Editing ◽  
Precision Agriculture ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Plant Genome ◽  
Trait Improvement ◽  
Challenges And Opportunities ◽  
Potential Applications ◽  
Regulation Strategies

Innovative plant breeding technology is an absolute necessity to enhance agriculture production in order to have an ambition of feeding nutritious food to the ever-increasing population. Current advances in CRISPR/Cas genome editing technology have led to effective targeted changes in most plants that promise to accelerate crop improvement. Here we discussed the discovery of CRISPR/Cas technology, associated manipulations for plant genome editing and its potential applications in the plant breeding. We emphasized mainly on the most essential applications of CRISPR/Cas genome editing in crop improvement, such as crop trait improvement (yield and biotic/abiotic stress tolerance), developments in optimizing gene regulation, strategies for generating virus resistance in plants, and the use of high throughput mutant libraries. Finally, the challenges and opportunities for plant breeding in precision agriculture and its bright future discussed.

scholarly journals Mutagenesis Approaches and Their Role in Crop Improvement

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 467 ◽  
Author(s):  
Juhi Chaudhary ◽  
Rupesh Deshmukh ◽  
Humira Sonah
Keyword(s):  
Genome Editing ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Zinc Finger Nucleases ◽  
Sequence Information ◽  
Whole Genome ◽  
Biotic And Abiotic Stress ◽  
Transcription Activator ◽  
Short Period ◽  
Induced Mutagenesis

Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such as physical, chemical, and insertional mutagen treatments; however, these methods are not preferred because of cost and tedious process. Nonetheless, with the advancements in next-generation sequencing (NGS) techniques, millions of mutations can be detected in a very short period of time and, therefore, considered as convenient and cost efficient. Furthermore, induced mutagenesis coupled with whole-genome sequencing has provided a robust platform for forward and reverse genetic applications. Moreover, the availability of whole-genome sequence information for large number of crops has enabled target-specific genome editing techniques as a preferable method to engineer desired mutations. The available genome editing approaches such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease have been utilized to perform site-specific mutations in several plant species. In particular, the CRISPR/Cas9 has transformed the genome editing because of its simplicity and robustness, therefore, have been utilized to enhance biotic and abiotic stress resistance. The Special Issue of Plants highlights the efforts by the scientific community utilizing mutagenesis techniques for the identification of novel genes toward crop improvement.

scholarly journals WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Dustin Cram ◽  
Manoj Kulkarni ◽  
Miles Buchwaldt ◽  
Nandhakishore Rajagopalan ◽  
Pankaj Bhowmik ◽  
...  
Keyword(s):  
Genome Editing ◽  
Web Application ◽  
Large Scale ◽  
Prediction Models ◽  
Crop Improvement ◽  
Collaborative Study ◽  
Regulation Of Gene Expression ◽  
Design Tool ◽  
Web Based ◽  
Target Activity

Abstract Background CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. Description We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184–191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. Conclusion The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/.

scholarly journals In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Menglong Chen ◽  
Hui Shi ◽  
Shixue Gou ◽  
Xiaomin Wang ◽  
Lei Li ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Mouse Model ◽  
Genome Editing ◽  
Large Scale ◽  
Gene Editing ◽  
High Efficiency ◽  
Muscle Fibers ◽  
Muscle Cells

Abstract Background Mutations in the DMD gene encoding dystrophin—a critical structural element in muscle cells—cause Duchenne muscular dystrophy (DMD), which is the most common fatal genetic disease. Clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing is a promising strategy for permanently curing DMD. Methods In this study, we developed a novel strategy for reframing DMD mutations via CRISPR-mediated large-scale excision of exons 46–54. We compared this approach with other DMD rescue strategies by using DMD patient-derived primary muscle-derived stem cells (DMD-MDSCs). Furthermore, a patient-derived xenograft (PDX) DMD mouse model was established by transplanting DMD-MDSCs into immunodeficient mice. CRISPR gene editing components were intramuscularly delivered into the mouse model by adeno-associated virus vectors. Results Results demonstrated that the large-scale excision of mutant DMD exons showed high efficiency in restoring dystrophin protein expression. We also confirmed that CRISPR from Prevotella and Francisella 1(Cas12a)-mediated genome editing could correct DMD mutation with the same efficiency as CRISPR-associated protein 9 (Cas9). In addition, more than 10% human DMD muscle fibers expressed dystrophin in the PDX DMD mouse model after treated by the large-scale excision strategies. The restored dystrophin in vivo was functional as demonstrated by the expression of the dystrophin glycoprotein complex member β-dystroglycan. Conclusions We demonstrated that the clinically relevant CRISPR/Cas9 could restore dystrophin in human muscle cells in vivo in the PDX DMD mouse model. This study demonstrated an approach for the application of gene therapy to other genetic diseases.

scholarly journals Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

2021 ◽  
Vol 22 (11) ◽  
pp. 5585
Author(s):  
Sajid Fiaz ◽  
Sunny Ahmar ◽  
Sajjad Saeed ◽  
Aamir Riaz ◽  
Freddy Mora-Poblete ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Food Security ◽  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Hybrid Seed Production ◽  
Biotic And Abiotic Stress ◽  
Transcription Activator ◽  
Protein System ◽  
Breeding Techniques

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

scholarly journals Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1359
Author(s):  
Javaria Tabassum ◽  
Shakeel Ahmad ◽  
Babar Hussain ◽  
Amos Musyoki Mawia ◽  
Aqib Zeb ◽  
...  
Keyword(s):  
Genome Editing ◽  
Crop Production ◽  
Grain Quality ◽  
High Efficiency ◽  
Abiotic Stress Tolerance ◽  
Mutation Breeding ◽  
Rice Grain ◽  
Rice Varieties ◽  
Rice Improvement ◽  
Breeding Techniques

Food crop production and quality are two major attributes that ensure food security. Rice is one of the major sources of food that feeds half of the world’s population. Therefore, to feed about 10 billion people by 2050, there is a need to develop high-yielding grain quality of rice varieties, with greater pace. Although conventional and mutation breeding techniques have played a significant role in the development of desired varieties in the past, due to certain limitations, these techniques cannot fulfill the high demands for food in the present era. However, rice production and grain quality can be improved by employing new breeding techniques, such as genome editing tools (GETs), with high efficiency. These tools, including clustered, regularly interspaced short palindromic repeats (CRISPR) systems, have revolutionized rice breeding. The protocol of CRISPR/Cas9 systems technology, and its variants, are the most reliable and efficient, and have been established in rice crops. New GETs, such as CRISPR/Cas12, and base editors, have also been applied to rice to improve it. Recombinases and prime editing tools have the potential to make edits more precisely and efficiently. Briefly, in this review, we discuss advancements made in CRISPR systems, base and prime editors, and their applications, to improve rice grain yield, abiotic stress tolerance, grain quality, disease and herbicide resistance, in addition to the regulatory aspects and risks associated with genetically modified rice plants. We also focus on the limitations and future prospects of GETs to improve rice grain quality.

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