Plant Genome Editing: Progress, Achievements, Applications and Future Prospects

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 37525

Special Issue Editors


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Guest Editor
Institute of Biology, Biotechnology and Environmental Protection; Faculty of Natural Sciences; University of Silesia in Katowice, 40-032 Katowice, Poland
Interests: plant genome editing; TILLING; phytohormones; strigolactones

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Guest Editor
Institute of Biology, Biotechnology and Environmental Protection; Faculty of Natural Sciences; University of Silesia in Katowice, 40-032 Katowice, Poland
Interests: plant genome editing; epigenetics; plant response to stresses

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Guest Editor
Centre of Plant Genome Engineering (CPGE), Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany
Interests: genome editing; targeted mutagenesis using customized endonucleases; genetic transformation of cereal plants; phytohormones; molecular farming; plant-microbe-interactions
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Special Issue Information

Dear Colleagues,

Targeted genome modification is a powerful tool in research that opens up new possibilities for directly targeting and modifying genomic sequences in a simple and effective way by accelerating gene function analysis and that can speed up the plant breeding process by introducing favorable alleles. A major breakthrough in this field was the adaptation of the prokaryotic immune system CRISPR/Cas (clustered, regularly interspaced short palindromic repeats and CRISPR-associated) for targeted genome modification. By combining the RNA- or DNA-binding property of the CRISPR/Cas system (nCas or dCas) with base conversion mediated by deaminases (BE or ABE), a further milestone in the field of genome editing could be achieved. Recently, a new technique called prime-editing was described, which allows the introduction of indels and all 12 base-to-base conversions (both transitions and transversions) without inducing DNA double-strand breaks. Currently, powerful systems are available for genome editing in plants. In addition, these techniques have been adapted for other purposes, such as the visualization of transcripts or the activation/repression of gene expression. New genome editing techniques are still being developed and improved for new plant species. In order to represent the great dynamics of the field, this Special Issue will collect articles (original research papers, perspectives, hypotheses, opinions, reviews, modeling approaches, and methods) that deal with the development, utilization, and application of plant genome editing.

Dr. Marek Marzec
Dr. Agnieszka Brąszewska
Dr. Götz Hensel
Guest Editors

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Keywords

  • Plant genome editing
  • CRISPR
  • Cas9
  • Cas12a
  • prime editing
  • dual base editors
  • TALEN
  • ZFN

Published Papers (4 papers)

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Research

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27 pages, 1329 KiB  
Article
Genome Editing in Crop Plant Research—Alignment of Expectations and Current Developments
by Meike Hüdig, Natalie Laibach and Anke-Christiane Hein
Plants 2022, 11(2), 212; https://doi.org/10.3390/plants11020212 - 14 Jan 2022
Cited by 5 | Viewed by 4565
Abstract
The rapid development of genome editing and other new genomic techniques (NGT) has evoked manifold expectations on purposes of the application of these techniques to crop plants. In this study, we identify and align these expectations with current scientific development. We apply a [...] Read more.
The rapid development of genome editing and other new genomic techniques (NGT) has evoked manifold expectations on purposes of the application of these techniques to crop plants. In this study, we identify and align these expectations with current scientific development. We apply a semi-quantitative text analysis approach on political, economic, and scientific opinion papers to disentangle and extract expectations towards the application of NGT-based plants. Using the sustainable development goals (SDG) of the 2030 agenda as categories, we identify contributions to food security or adaptation to climatic changes as the most frequently mentioned expectations, accompanied by the notion of sustainable agriculture and food systems. We then link SDG with relevant plant traits and review existing research and commercial field trials for genome-edited crop plants. For a detailed analysis we pick as representative traits drought tolerance and resistance against fungal pathogens. Diverse genetic setscrews for both traits have been identified, modified, and tested under laboratory conditions, although there are only a few in the field. All in all, NGT-plants that can withstand more than one stressor or different environments are not documented in advanced development states. We further conclude that developing new plants with modified traits will not be sufficient to reach food security or adaption to climatic changes in a short time frame. Further scientific development of sustainable agricultural systems will need to play an important role to tackle SDG challenges, as well. Full article
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Review

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39 pages, 4451 KiB  
Review
Hairy CRISPR: Genome Editing in Plants Using Hairy Root Transformation
by Alexey S. Kiryushkin, Elena L. Ilina, Elizaveta D. Guseva, Katharina Pawlowski and Kirill N. Demchenko
Plants 2022, 11(1), 51; https://doi.org/10.3390/plants11010051 - 24 Dec 2021
Cited by 25 | Viewed by 10232
Abstract
CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline [...] Read more.
CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline the current state of the art reached by the combination of these approaches over seven years. Additionally, we discuss the origins of different Agrobacterium rhizogenes strains that are widely used for hairy root transformation; the components of CRISPR/Cas vectors, such as the promoters that drive Cas or gRNA expression, the types of Cas nuclease, and selectable and screenable markers; and the application of CRISPR/Cas genome editing in hairy roots. The modification of the already known vector pKSE401 with the addition of the rice translational enhancer OsMac3 and the gene encoding the fluorescent protein DsRed1 is also described. Full article
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22 pages, 3670 KiB  
Review
CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences
by Chou Khai Soong Karlson, Siti Nurfadhlina Mohd-Noor, Nadja Nolte and Boon Chin Tan
Plants 2021, 10(10), 2055; https://doi.org/10.3390/plants10102055 - 29 Sep 2021
Cited by 34 | Viewed by 8444
Abstract
RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional [...] Read more.
RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement. Full article
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24 pages, 4497 KiB  
Review
Herbicide Resistance: Another Hot Agronomic Trait for Plant Genome Editing
by Amjad Hussain, Xiao Ding, Muna Alariqi, Hakim Manghwar, Fengjiao Hui, Yapei Li, Junqi Cheng, Chenglin Wu, Jinlin Cao and Shuangxia Jin
Plants 2021, 10(4), 621; https://doi.org/10.3390/plants10040621 - 24 Mar 2021
Cited by 27 | Viewed by 12837
Abstract
Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a [...] Read more.
Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a rapidly increasing human population. Chemical weed control (herbicides) along with integrated weed management (IWM) practices can be the most effective and reliable method of weed management programs. The application of herbicides for weed control practices calls for the urgency to develop herbicide-resistant (HR) crops. Recently, genome editing tools, especially CRISPR-Cas9, have brought innovation in genome editing technology that opens up new possibilities to provide sustainable farming in modern agricultural industry. To date, several non-genetically modified (GM) HR crops have been developed through genome editing that can present a leading role to combat weed problems along with increasing crop productivity to meet increasing food demand around the world. Here, we present the chemical method of weed control, approaches for herbicide resistance development, and possible advantages and limitations of genome editing in herbicide resistance. We also discuss how genome editing would be effective in combating intensive weed problems and what would be the impact of genome-edited HR crops in agriculture. Full article
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