scholarly journals Genome Editing in Cereals: Approaches, Applications and Challenges

2020 ◽  
Vol 21 (11) ◽  
pp. 4040 ◽  
Author(s):  
Waquar A. Ansari ◽  
Sonali U. Chandanshive ◽  
Vacha Bhatt ◽  
Altafhusain B. Nadaf ◽  
Sanskriti Vats ◽  
...  
Keyword(s):  
Genome Editing ◽  
Target Genes ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Cereal Crops ◽  
Sequence Information ◽  
World Population ◽  
Base Editing ◽  
Crop Varieties ◽  
Current Scenario

Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising world population particularly under vulnerable climatic condition, development of high yielding stress tolerant crops is needed. In this regard, technologies upgradation in the field of genome editing looks promising. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is a rapidly growing genome editing technique being effectively applied in different organisms, that includes both model and crop plants. In recent times CRISPR/Cas9 is being considered as a technology which revolutionized fundamental as well as applied research in plant breeding. Genome editing using CRISPR/Cas9 system has been successfully demonstrated in many cereal crops including rice, wheat, maize, and barley. Availability of whole genome sequence information for number of crops along with the advancement in genome-editing techniques provides several possibilities to achieve desirable traits. In this review, the options available for crop improvement by implementing CRISPR/Cas9 based genome-editing techniques with special emphasis on cereal crops have been summarized. Recent advances providing opportunities to simultaneously edit many target genes were also discussed. The review also addressed recent advancements enabling precise base editing and gene expression modifications. In addition, the article also highlighted limitations such as transformation efficiency, specific promoters and most importantly the ethical and regulatory issues related to commercial release of novel crop varieties developed through genome editing.

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 Base Editing in Plants: Applications, Challenges, and Future Prospects

2021 ◽  
Vol 12 ◽  
Author(s):  
Mawuli K. Azameti ◽  
Wadzani Palnam Dauda
Keyword(s):  
Genome Editing ◽  
Crop Production ◽  
Agronomic Traits ◽  
New Technology ◽  
Crop Improvement ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Base Editing ◽  
Crop Varieties

The ability to create targeted modifications in the genomes of plants using genome editing technologies has revolutionized research in crop improvement in the current dispensation of molecular biology. This technology has attracted global attention and has been employed in functional analysis studies in crop plants. Since many important agronomic traits are confirmed to be determined by single-nucleotide polymorphisms, improved crop varieties could be developed by the programmed and precise conversion of targeted single bases in the genomes of plants. One novel genome editing approach which serves for this purpose is base editing. Base editing directly makes targeted and irreversible base conversion without creating double-strand breaks (DSBs). This technology has recently gained quick acceptance and adaptation because of its precision, simplicity, and multiplex capabilities. This review focuses on generating different base-editing technologies and how efficient they are in editing nucleic acids. Emphasis is placed on the exploration and applications of these base-editing technologies to enhance crop production. The review also highlights the drawbacks and the prospects of this new technology.

scholarly journals Precision Genome Engineering Through Cytidine Base Editing in Rapeseed (Brassica napus. L)

2020 ◽  
Vol 2 ◽  
Author(s):  
Limin Hu ◽  
Olalekan Amoo ◽  
Qianqian Liu ◽  
Shengli Cai ◽  
Miaoshan Zhu ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Molecular Breeding ◽  
Target Genes ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Brassica Napus L ◽  
Editing Efficiency ◽  
Base Editing ◽  
Expected Gain ◽  
Genome Wide

Rapeseed is one of the world's most important sources of oilseed crops. Single nucleotide substitution is the basis of most genetic variation underpinning important agronomic traits. Therefore, genome-wide and target-specific base editing will greatly facilitate precision plant molecular breeding. In this study, four CBE systems (BnPBE, BnA3A-PBE, BnA3A1-PBE, and BnPBGE14) were modified to achieve cytidine base editing at five target genes in rapeseed. The results indicated that genome editing is achievable in three CBEs systems, among which BnA3A1-PBE had the highest base-editing efficiency (average 29.8% and up to 50.5%) compared to all previous CBEs reported in rapeseed. The editing efficiency of BnA3A1-PBE is ~8.0% and fourfold higher, than those of BnA3A-PBE (averaging 27.6%) and BnPBE (averaging 6.5%), respectively. Moreover, BnA3A1-PBE and BnA3A-PBE could significantly increase the proportion of both the homozygous and biallelic genotypes, and also broaden the editing window compared to BnPBE. The cytidine substitution which occurred at the target sites of both BnaA06.RGA and BnaALS were stably inherited and conferred expected gain-of-function phenotype in the T1 generation (i.e., dwarf phenotype or herbicide resistance for weed control, respectively). Moreover, new alleles or epialleles with expected phenotype were also produced, which served as an important resource for crop improvement. Thus, the improved CBE system in the present study, BnA3A1-PBE, represents a powerful base editor for both gene function studies and molecular breeding in rapeseed.

scholarly journals Base editing in Streptomyces with Cas9-deaminase fusions

2019 ◽  
Author(s):  
Zhiyu Zhong ◽  
Junhong Guo ◽  
Liang Deng ◽  
Li Chen ◽  
Jian Wang ◽  
...  
Keyword(s):  
Genome Editing ◽  
Target Genes ◽  
Genetic Manipulation ◽  
Strand Break ◽  
High Fidelity ◽  
Nucleotide Substitutions ◽  
Base Editing ◽  
Dna Double Strand Break ◽  
Repair Template ◽  
Adenine Base

AbstractConventional CRISPR/Cas genetic manipulation has been profitably applied to the genus Streptomyces, the most prolific bacterial producers of antibiotics. However, its reliance on DNA double-strand break (DSB) formation leads to unacceptably low yields of desired recombinants. We have adapted for Streptomyces recently-introduced cytidine base editors (CBEs) and adenine base editors (ABEs) which enable targeted C-to-T or A-to-G nucleotide substitutions, respectively, bypassing DSB and the need for a repair template. We report successful genome editing in Streptomyces at frequencies of around 50% using defective Cas9-guided base editors and up to 100% by using nicked Cas9-guided base editors. Furthermore, we demonstrate the multiplex genome editing potential of the nicked Cas9-guided base editor BE3 by programmed mutation of nine target genes simultaneously. Use of the high-fidelity version of BE3 (HF-BE3) essentially improved editing specificity. Collectively, this work provides a powerful new tool for genome editing in Streptomyces.

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 CRISPR/Cas9-Mediated Multiplex Genome Editing of the BnWRKY11 and BnWRKY70 Genes in Brassica napus L.

2018 ◽  
Vol 19 (9) ◽  
pp. 2716 ◽  
Author(s):  
Qinfu Sun ◽  
Li Lin ◽  
Dongxiao Liu ◽  
Dewei Wu ◽  
Yujie Fang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Transgenic Plants ◽  
Genome Editing ◽  
Target Genes ◽  
High Efficiency ◽  
Pathogenic Fungus ◽  
Crop Improvement ◽  
Brassica Napus L ◽  
Significant Difference ◽  
Genomic Editing

Targeted genome editing is a desirable means of basic science and crop improvement. The clustered, regularly interspaced, palindromic repeat (CRISPR)/Cas9 (CRISPR-associated 9) system is currently the simplest and most commonly used system in targeted genomic editing in plants. Single and multiplex genome editing in plants can be achieved under this system. In Arabidopsis, AtWRKY11 and AtWRKY70 genes were involved in JA- and SA-induced resistance to pathogens, in rapeseed (Brassica napus L.), BnWRKY11 and BnWRKY70 genes were found to be differently expressed after inoculated with the pathogenic fungus, Sclerotinia sclerotiorum (Lib.) de Bary. In this study, two Cas9/sgRNA constructs targeting two copies of BnWRKY11 and four copies of BnWRKY70 were designed to generate BnWRKY11 and BnWRKY70 mutants respectively. As a result, twenty-two BnWRKY11 and eight BnWRKY70 independent transformants (T0) were obtained, with the mutation ratios of 54.5% (12/22) and 50% (4/8) in BnWRKY11 and BnWRKY70 transformants respectively. Eight and two plants with two copies of mutated BnWRKY11 and BnWRKY70 were obtained respectively. In T1 generation of each plant examined, new mutations on target genes were detected with high efficiency. The vast majority of BnWRKY70 mutants showed editing in three copies of BnWRKY70 in examined T1 plants. BnWRKY70 mutants exhibited enhanced resistance to Sclerotinia, while BnWRKY11 mutants showed no significant difference in Sclerotinia resistance when compared to non-transgenic plants. In addition, plants that overexpressed BnWRKY70 showed increased sensitivity when compared to non-transgenic plants. Altogether, our results demonstrated that BnWRKY70 may function as a regulating factor to negatively control the Sclerotinia resistance and CRISPR/Cas9 system could be used to generate germplasm in B. napus with high resistance against Sclerotinia.

scholarly journals Application of genome editing tools in plants

2021 ◽  
Vol 19 (1) ◽  
pp. 15-40
Author(s):  
Nguyen Duc Thanh
Keyword(s):  
Genome Editing ◽  
Target Gene ◽  
Crop Improvement ◽  
Double Sequence ◽  
Targeted Mutagenesis ◽  
Nonhomologous End Joining ◽  
Transcription Activator ◽  
End Joining ◽  
Base Editing ◽  
Living Organisms

Genome editing technology is the genome modification techniques, such as targeted mutagenesis or insert/delete/replacement at specific locations in the genome of living organisms. Genome editing is based on the creation of double sequence break (DSB) in a specific location and DNA repair via nonhomologous end joining (NHEJ) or homology direct repair (HDR). The development of sequence-specific nuclease (SSN) allows precise editing of the target gene. These SSNs include: meganuclease (MN), zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and CRISPR-associated nuclease (Cas) including CRISPR/Cas9 (from Streptococcus pyogenes) and CRISPR/Cpf1 (from Prevoltella and Francisella1). These are the genome editing tools used to create DSBs at specific locations of the genome. Recently, the base editing (BE) and prime editing (PE) tools have been reported. This review will cover the basics of these tools and their application in genome editing in plants, especially providing the most up-to-date information on their application in crop improvement.

scholarly journals Genome Editing: An Emerging Tool for Plant Breeders

2020 ◽  
Author(s):  
Anand Kumar ◽  
Karansher Sandhu
Keyword(s):  
Genome Editing ◽  
Gene Editing ◽  
Biotic Resistance ◽  
New Technology ◽  
Crop Improvement ◽  
Modern Society ◽  
New Era ◽  
Crop Varieties ◽  
Gene Information ◽  
Adenine Base

Conventional plant breeding has contributed enormously towards feeding the world and has played crucial roles in the development of modern society. The conventional method creates variation by transferring genes between or within the species. In general, these methods are more expensive and takes more time, to overcome these limitations, new technology is required. Genome editing is a powerful tool for biotechnology applications, with the capacity to alter the function of any gene. With the availability of gene information for the majority of the traits, genome editing emerged as a potential to create a new variation with the introduction of any transgene. The important genome editing tools used nowadays are ZFNs, TALEN, Pentatricopeptide repeats protein, adenine base editor, RNA interference, and CRISPR/Cas9. These tools have opened a new era for crop improvement. Due to the complex genetic architecture of most traits, it is challenging to edit genes controlling them. To overcome these challenges, genome editing provides a broader perspective. Among the above-mentioned tools, CRISPR/Cas9 is the most powerful tool for gene editing. These technologies are being used to create abiotic and biotic resistance crop varieties.

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

2021 ◽  
Vol 11 ◽  
Author(s):  
Leena Tripathi ◽  
Valentine Otang Ntui ◽  
Jaindra Nath Tripathi ◽  
P. Lava Kumar
Keyword(s):  
Genome Editing ◽  
Cost Effective ◽  
Whole Genome Sequence ◽  
Viral Diseases ◽  
Regeneration System ◽  
Banana Production ◽  
Crop Varieties ◽  
Resistant Varieties ◽  
Effective Option ◽  
Negative Impacts

Viral diseases are significant biotic constraints for banana (Musa spp.) production as they affect the yield and limit the international movement of germplasm. Among all the viruses known to infect banana, the banana bunchy top virus and banana streak viruses are widespread and economically damaging. The use of virus-resistant bananas is the most cost-effective option to minimize the negative impacts of viral-diseases on banana production. CRISPR/Cas-based genome editing is emerging as the most powerful tool for developing virus-resistant crop varieties in several crops, including the banana. The availability of a vigorous genetic transformation and regeneration system and a well-annotated whole-genome sequence of banana makes it a compelling candidate for genome editing. A robust CRISPR/Cas9-based genome editing of the banana has recently been established, which can be applied in developing disease-resistant varieties. Recently, the CRISPR system was exploited to detect target gene sequences using Cas9, Cas12, Cas13, and Cas14 enzymes, thereby unveiling the use of this technology for virus diagnosis. This article presents a synopsis of recent advancements and perspectives on the application of CRISPR/Cas-based genome editing for diagnosing and developing resistance against banana viruses and challenges in genome-editing of banana.

scholarly journals Multiplex nucleotide editing by high-fidelity Cas9 variants with improved efficiency in rice

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Wen Xu ◽  
Wei Song ◽  
Yongxing Yang ◽  
Ying Wu ◽  
Xinxin Lv ◽  
...  
Keyword(s):  
Genome Editing ◽  
Genome Engineering ◽  
Crop Improvement ◽  
High Fidelity ◽  
Knock Out ◽  
Base Editing ◽  
Guide Rna ◽  
Genome Modification ◽  
Targeted Genome Modification ◽  
Target Effect

Abstract Background Application of the CRISPR/Cas9 system or its derived base editors enables targeted genome modification, thereby providing a programmable tool to exploit gene functions and to improve crop traits. Results We report that PmCDA1 is much more efficient than rAPOBEC1 when fused to CRISPR/Cas9 nickase for the conversion of cytosine (C) to thymine (T) in rice. Three high-fidelity SpCas9 variants, eSpCas9(1.1), SpCas9-HF2 and HypaCas9, were engineered to serve with PmCDA1 (pBEs) as C-to-T base editors. These three high-fidelity editors had distinct multiplex-genome editing efficiencies. To substantially improve their base-editing efficiencies, a tandemly arrayed tRNA-modified single guide RNA (sgRNA) architecture was applied. The efficiency of eSpCas9(1.1)-pBE was enhanced up to 25.5-fold with an acceptable off-target effect. Moreover, two- to five-fold improvement was observed for knock-out mutation frequency by these high-fidelity Cas9s under the direction of the tRNA-modified sgRNA architecture. Conclusions We have engineered a diverse toolkit for efficient and precise genome engineering in rice, thus making genome editing for plant research and crop improvement more flexible.

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