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CRISPR-Mediated Base Editing in Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 17832

Special Issue Editor

Department of Medical & Biological Sciences, The Catholic University of Kore, Bucheon, Gyeonggi-do 14662, Republic of Korea
Interests: plant genomics; natural variation; genome editing; CRISPR; base editing; bioinformatics; genotyping by sequencing; natural selection and adaptation

Special Issue Information

Dear Colleagues,

CRISPR-mediated genome editing has been a core technique in most fields of biological research. Inducing mostly short in/del mutations by double strand breaks with CRISPR/Cas9 guided with single strand guide RNA results in the loss of function of target genes. Furthermore, the recent emergence of base editing tools using the CRISPR system with Cas9 variants and fused deaminase broadens the possibility of studies on gene functions and traits via changing amino acids compositions in target proteins.

In this Special Issue, we would like to give an opportunity to researchers to introduce their results using various types of CRISPR-mediated base editing in plants. Many research topics relating to base editing, such as phenotypic validation of base substitution mutations, specific testing of CRISPR-base editing tools to improve efficiency, and functional prediction based on base modification, are welcome. Additionally, we will consider publication of manuscripts dealing with genome editing research in the plant system.

Dr. Sang-Tae Kim
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

  • genome editing
  • base editing
  • plant
  • CRISPR
  • Cas9
  • dCas9
  • guide RNA
  • programmable nuclease
  • cytosine base editor
  • adenine base editor
  • prime editor
  • genome engineering
  • crops

Published Papers (4 papers)

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Research

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13 pages, 4632 KiB  
Article
CRISPR/Cas9-Mediated Targeted Mutagenesis of BnaCOL9 Advances the Flowering Time of Brassica napus L.
by Jian Guo, Lei Zeng, Hui Chen, Chaozhi Ma, Jinxing Tu, Jinxiong Shen, Jing Wen, Tingdong Fu and Bin Yi
Int. J. Mol. Sci. 2022, 23(23), 14944; https://doi.org/10.3390/ijms232314944 - 29 Nov 2022
Cited by 2 | Viewed by 1579
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. The planting area and output of rapeseed are affected by the flowering time, which is a critical agronomic feature. COL9 controls growth and development in many different [...] Read more.
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. The planting area and output of rapeseed are affected by the flowering time, which is a critical agronomic feature. COL9 controls growth and development in many different plant species as a member of the zinc finger transcription factor family. However, BnaCOL9 in rapeseed has not been documented. The aim of this study was to apply CRISPR/Cas9 technology to create an early-flowering germplasm resource to provide useful material for improving the early-maturing breeding of rapeseed. We identified four COL9 homologs in rapeseed that were distributed on chromosomes A05, C05, A03, and C03. We successfully created quadruple BnaCOL9 mutations in rapeseed using the CRISPR/Cas9 platform. The quadruple mutants of BnaCOL9 flowered earlier than the wild-type. On the other hand, the flowering time of the BnaCOL9 overexpression lines was delayed. An analysis of the expression patterns revealed that these genes were substantially expressed in the leaves and flowers. A subcellular localization experiment demonstrated that BnaCOL9 was in the nucleus. Furthermore, we discovered that two key flowering-related genes, BnaCO and BnaFT, were highly elevated in the BnaCOL9 mutants, but dramatically downregulated in the BnaCOL9 overexpression lines. Our findings demonstrate that BnaCOL9 is a significant flowering inhibitor in rapeseed and may be employed as a crucial gene for early-maturing breeding. Full article
(This article belongs to the Special Issue CRISPR-Mediated Base Editing in Plants)
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15 pages, 8348 KiB  
Article
Using Multiplexed CRISPR/Cas9 for Suppression of Cotton Leaf Curl Virus
by Barkha Binyameen, Zulqurnain Khan, Sultan Habibullah Khan, Aftab Ahmad, Nayla Munawar, Muhammad Salman Mubarik, Hasan Riaz, Zulfiqar Ali, Asif Ali Khan, Alaa T. Qusmani, Kamel A. Abd-Elsalam and Sameer H. Qari
Int. J. Mol. Sci. 2021, 22(22), 12543; https://doi.org/10.3390/ijms222212543 - 21 Nov 2021
Cited by 15 | Viewed by 3485
Abstract
In recent decades, Pakistan has suffered a decline in cotton production due to several factors, including insect pests, cotton leaf curl disease (CLCuD), and multiple abiotic stresses. CLCuD is a highly damaging plant disease that seriously limits cotton production in Pakistan. Recently, genome [...] Read more.
In recent decades, Pakistan has suffered a decline in cotton production due to several factors, including insect pests, cotton leaf curl disease (CLCuD), and multiple abiotic stresses. CLCuD is a highly damaging plant disease that seriously limits cotton production in Pakistan. Recently, genome editing through CRISPR/Cas9 has revolutionized plant biology, especially to develop immunity in plants against viral diseases. Here we demonstrate multiplex CRISPR/Cas-mediated genome editing against CLCuD using transient transformation in N. benthamiana plants and cotton seedlings. The genomic sequences of cotton leaf curl viruses (CLCuVs) were obtained from NCBI and the guide RNA (gRNA) were designed to target three regions in the viral genome using CRISPR MultiTargeter. The gRNAs were cloned in pHSE401/pKSE401 containing Cas9 and confirmed through colony PCR, restriction analysis, and sequencing. Confirmed constructs were moved into Agrobacterium and subsequently used for transformation. Agroinfilteration in N. benthamiana revealed delayed symptoms (3–5 days) with improved resistance against CLCuD. In addition, viral titer was also low (20–40%) in infected plants co-infiltrated with Cas9-gRNA, compared to control plants (infected with virus only). Similar results were obtained in cotton seedlings. The results of transient expression in N. benthamiana and cotton seedlings demonstrate the potential of multiplex CRISPR/Cas to develop resistance against CLCuD. Five transgenic plants developed from three experiments showed resistance (60−70%) to CLCuV, out of which two were selected best during evaluation and screening. The technology will help breeding CLCuD-resistant cotton varieties for sustainable cotton production. Full article
(This article belongs to the Special Issue CRISPR-Mediated Base Editing in Plants)
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Review

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40 pages, 3776 KiB  
Review
An Outlook on Global Regulatory Landscape for Genome-Edited Crops
by Aftab Ahmad, Nayla Munawar, Zulqurnain Khan, Alaa T. Qusmani, Sultan Habibullah Khan, Amer Jamil, Sidra Ashraf, Muhammad Zubair Ghouri, Sabin Aslam, Muhammad Salman Mubarik, Ahmad Munir, Qaiser Sultan, Kamel A. Abd-Elsalam and Sameer H. Qari
Int. J. Mol. Sci. 2021, 22(21), 11753; https://doi.org/10.3390/ijms222111753 - 29 Oct 2021
Cited by 31 | Viewed by 5467
Abstract
The revolutionary technology of CRISPR/Cas systems and their extraordinary potential to address fundamental questions in every field of biological sciences has led to their developers being awarded the 2020 Nobel Prize for Chemistry. In agriculture, CRISPR/Cas systems have accelerated the development of new [...] Read more.
The revolutionary technology of CRISPR/Cas systems and their extraordinary potential to address fundamental questions in every field of biological sciences has led to their developers being awarded the 2020 Nobel Prize for Chemistry. In agriculture, CRISPR/Cas systems have accelerated the development of new crop varieties with improved traits—without the need for transgenes. However, the future of this technology depends on a clear and truly global regulatory framework being developed for these crops. Some CRISPR-edited crops are already on the market, and yet countries and regions are still divided over their legal status. CRISPR editing does not require transgenes, making CRISPR crops more socially acceptable than genetically modified crops, but there is vigorous debate over how to regulate these crops and what precautionary measures are required before they appear on the market. This article reviews intended outcomes and risks arising from the site-directed nuclease CRISPR systems used to improve agricultural crop plant genomes. It examines how various CRISPR system components, and potential concerns associated with CRISPR/Cas, may trigger regulatory oversight of CRISPR-edited crops. The article highlights differences and similarities between GMOs and CRISPR-edited crops, and discusses social and ethical concerns. It outlines the regulatory framework for GMO crops, which many countries also apply to CRISPR-edited crops, and the global regulatory landscape for CRISPR-edited crops. The article concludes with future prospects for CRISPR-edited crops and their products. Full article
(This article belongs to the Special Issue CRISPR-Mediated Base Editing in Plants)
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22 pages, 1804 KiB  
Review
Exosome/Liposome-like Nanoparticles: New Carriers for CRISPR Genome Editing in Plants
by Mousa A. Alghuthaymi, Aftab Ahmad, Zulqurnain Khan, Sultan Habibullah Khan, Farah K. Ahmed, Sajid Faiz, Eugenie Nepovimova, Kamil Kuča and Kamel A. Abd-Elsalam
Int. J. Mol. Sci. 2021, 22(14), 7456; https://doi.org/10.3390/ijms22147456 - 12 Jul 2021
Cited by 32 | Viewed by 6276
Abstract
Rapid developments in the field of plant genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems necessitate more detailed consideration of the delivery of the CRISPR system into plants. Successful and safe editing of plant genomes is partly based [...] Read more.
Rapid developments in the field of plant genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems necessitate more detailed consideration of the delivery of the CRISPR system into plants. Successful and safe editing of plant genomes is partly based on efficient delivery of the CRISPR system. Along with the use of plasmids and viral vectors as cargo material for genome editing, non-viral vectors have also been considered for delivery purposes. These non-viral vectors can be made of a variety of materials, including inorganic nanoparticles, carbon nanotubes, liposomes, and protein- and peptide-based nanoparticles, as well as nanoscale polymeric materials. They have a decreased immune response, an advantage over viral vectors, and offer additional flexibility in their design, allowing them to be functionalized and targeted to specific sites in a biological system with low cytotoxicity. This review is dedicated to describing the delivery methods of CRISPR system into plants with emphasis on the use of non-viral vectors. Full article
(This article belongs to the Special Issue CRISPR-Mediated Base Editing in Plants)
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