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Cells
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Plant Genome Editing: State-of-the-Art and Perspectives in China
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Plant Genome Editing: State-of-the-Art and Perspectives in China

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: closed (1 May 2023) | Viewed by 26067

Special Issue Editors

Prof. Dr. Shuangxia Jin

E-Mail Website
Guest Editor
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Interests: cotton biotechnology; insects and cotton host molecular interaction; plant genome editing; plant genomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yan Wenhao

E-Mail Website
Guest Editor
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Interests: wheat regulome and yield genetics; plant biotechnology; plant development and single cell biology

Special Issue Information

Dear Colleagues,

Since 2012, efficient genome editing systems (TALEN, CRISPRs) has been developed for a wide range of plant species and was becoming a standard experimental strategy in most research labs. Genome editing with engineered nucleases will likely contribute to many fields of plant sciences from basic research and plant breeding. Progress in genome editing are stimulating plant genome studies at an unprecedented pace.

Cells will focus on new insights into genome editing opinions, methods and policy with a special issue that exhibits exciting findings in all areas of plant sciences in China. The special issue will prefer comprehensive reviews and original articles manuscripts presenting significant progress that highlight the biological insights in question, including (but not limited to) in the following areas:

  • Gene knock out
  • Gene knock in
  • Gene knock down
  • Transcription activation
  • Base editing
  • Prime editing
  • New CRISPRs variants
  • High-throughput genome editing system
  • Off-target analysis
  • Genome editing assisted plant breeding
  • Policy, regulation for the genome editing products

Prof. Dr. Shuangxia Jin
Prof. Dr. Yan Wenhao
Guest Editors

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant
  • genome editing
  • CRISPR/Cas
  • knock in
  • transcription activation
  • base editing
  • prime editing
  • off-target
  • molecular breeding

Published Papers (7 papers)

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Research

Jump to: Review, Other

17 pages, 3737 KiB  
Article
Editing of a Novel Cd Uptake-Related Gene CUP1 Contributes to Reducing Cd Accumulations in Arabidopsis thaliana and Brassica napus
by Junyu Yao, Jiuyuan Bai, Sha Liu, Jingyan Fu, Ying Zhang, Tianshun Luo, Hongpei Ren, Rui Wang and Yun Zhao
Cells 2022, 11(23), 3888; https://doi.org/10.3390/cells11233888 - 01 Dec 2022
Cited by 3 | Viewed by 1815
Abstract
Brassica napus is a Cd hyperaccumulator, which is a serious threat to food and fodder safety. However, no related studies on developing Cd-safe B. napus have been reported yet. Here, we screened out a novel Cd uptake-related gene, AtCUP1, from the major facilitator [...] Read more.
Brassica napus is a Cd hyperaccumulator, which is a serious threat to food and fodder safety. However, no related studies on developing Cd-safe B. napus have been reported yet. Here, we screened out a novel Cd uptake-related gene, AtCUP1, from the major facilitator superfamily in Arabidopsis thaliana. The mutation of AtCUP1 decreased Cd accumulation, both in roots and shoots of A. thaliana. Furthermore, the disruption of the AtCUP1 gene by the CRISPR/Cas9 system significantly reduced Cd accumulation in A. thaliana. Interestingly, the disruption of the BnCUP1 gene, an orthologous gene of AtCUP1, by the CRISPR/Cas9 system also diminished Cd accumulation in both roots and shoots of B. napus based on the hydroponics assay. Furthermore, for the field experiment, the Cd accumulations of BnCUP1-edited lines were reduced by 52% in roots and 77% in shoots compared to that of wild-type (WT) lines, and the biomass and yield of BnCUP1-edited lines increased by 42% and 47% of that of WT, respectively. Noteworthily, agronomic characteristics of B. napus were not apparently affected by BnCUP1-editing. Thus, BnCUP1-edited lines are excellent non-transgenic germplasm resources for reducing Cd accumulation without a distinct compromise in yield, which could be applied to agricultural production in Cd-contaminated soils. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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13 pages, 3666 KiB  
Article
Highly Efficient Genome Editing Using Geminivirus-Based CRISPR/Cas9 System in Cotton Plant
by Bo Li, Chunyang Fu, Jiawei Zhou, Fengjiao Hui, Qiongqiong Wang, Fuqiu Wang, Guanying Wang, Zhongping Xu, Lianlian Che, Daojun Yuan, Yanqin Wang, Xianlong Zhang and Shuangxia Jin
Cells 2022, 11(18), 2902; https://doi.org/10.3390/cells11182902 - 16 Sep 2022
Cited by 9 | Viewed by 3449
Abstract
Upland cotton (Gossypium hirsutum), an allotetraploid, contains At- and Dt- subgenome and most genes have multiple homologous copies, which pose a huge challenge to investigate genes’ function due to the functional redundancy. Therefore, it is of great significance to establish effective [...] Read more.
Upland cotton (Gossypium hirsutum), an allotetraploid, contains At- and Dt- subgenome and most genes have multiple homologous copies, which pose a huge challenge to investigate genes’ function due to the functional redundancy. Therefore, it is of great significance to establish effective techniques for the functional genomics in cotton. In this study, we tested two novel genome editing vectors and compared them with the CRISPR/Cas9 system (pRGEB32-GhU6.7) developed in our laboratory previously. In the first new vector, the sgRNA transcription unite was constructed into the replicon (LIR-Donor-SIR-Rep-LIR) of the bean yellow dwarf virus (BeYDV) and named as pBeYDV-Cas9-KO and in the second vector, the ubiquitin promoter that drives Cas9 protein was replaced with a constitutive CaMV 35S promoter and defined as pRGEB32-35S. The results from transgenic cotton calli/plants revealed that pBeYDV-Cas9-KO vector showed the highest editing efficiency of GhCLA1 in At and Dt subgenomes edited simultaneously up to 73.3% compared to the 44.6% of pRGEB32-GhU6.7 and 51.2% of pRGEB32-35S. The editing efficiency of GhCLA1 in At and Dt subgenome by pBeYDV-Cas9-KO was 85.7% and 97.2%, respectively, whereas the efficiency by pRGEB32-GhU6.7 and pRGEB32-35S vectors was 67.7%, 86.5%, 84%, and 87.2%, respectively. The editing profile of pBeYDV-Cas9-KO was mainly composed of fragment deletion, accounting for 84.0% and ranging 1–10 bp in length. The main editing sites are located at positions 11–17 upstream of PAM site. The off-target effects were not detected in all potential off-target sites. Taken together, the pBeYDV-Cas9-KO system has high editing efficiency and specificity with wide editing range than the traditional CRISPR/Cas9 system, which provides a powerful tool for cotton functional genomics research and molecular breeding. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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14 pages, 2694 KiB  
Article
Improvement of Bacterial Blight Resistance in Two Conventionally Cultivated Rice Varieties by Editing the Noncoding Region
by Changyan Li, Lei Zhou, Bian Wu, Sanhe Li, Wenjun Zha, Wei Li, Zaihui Zhou, Linfeng Yang, Lei Shi, Yongjun Lin and Aiqing You
Cells 2022, 11(16), 2535; https://doi.org/10.3390/cells11162535 - 16 Aug 2022
Cited by 4 | Viewed by 2763
Abstract
xa13 is a recessive pleiotropic gene that positively regulates rice disease resistance and negatively regulates rice fertility; thus, seriously restricting its rice breeding application. In this study, CRISPR/Cas9 gene-editing technology was used to delete the Xa13 gene promoter partial sequence, including the pathogenic [...] Read more.
xa13 is a recessive pleiotropic gene that positively regulates rice disease resistance and negatively regulates rice fertility; thus, seriously restricting its rice breeding application. In this study, CRISPR/Cas9 gene-editing technology was used to delete the Xa13 gene promoter partial sequence, including the pathogenic bacteria-inducible expression element. Rice with the edited promoter region lost the ability for pathogen-induced gene expression without affecting background gene expression in leaves and anthers, resulting in disease resistance and normal yield. The study also screened a family of disease-resistant and normal fertile plants in which the target sequence was deleted and the exogenous transgene fragment isolated in the T1 generation (transgene-free line). Important agronomic traits of the T2 generation rice were examined. T2 generation rice with/without exogenous DNA showed no statistical differences compared to the wild type in heading stage, plant height, panicles per plant, panicle length, or seed setting rate in the field. Two important conventional rice varieties, namely Kongyu131 (KY131, Geng/japonica) and Huanghuazhan (HHZ, Xian/indica), were successfully transformed, and disease-resistant and fertile materials were obtained. Currently, these are the two important conventional rice varieties in China that can be used directly for production after improvement. Expression of the Xa13 gene in the leaves of transgenic rice (KY-PD and HHZ-PD) was not induced after pathogen infection, indicating that this method can be used universally and effectively to promote the practical application of xa13, a recessive disease-resistant pleiotropic gene, for rice bacterial blight resistance. Our study on the regulation of gene expression by editing noncoding regions of the genes provides a new idea for the development of molecular design breeding in the future. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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Review

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28 pages, 2453 KiB  
Review
CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives
by Yaxin Wang, Naeem Zafar, Qurban Ali, Hakim Manghwar, Guanying Wang, Lu Yu, Xiao Ding, Fang Ding, Ni Hong, Guoping Wang and Shuangxia Jin
Cells 2022, 11(23), 3928; https://doi.org/10.3390/cells11233928 - 05 Dec 2022
Cited by 14 | Viewed by 6047
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with [...] Read more.
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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16 pages, 1034 KiB  
Review
Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants
by Xiao Ding, Lu Yu, Luo Chen, Yujie Li, Jinlun Zhang, Hanyan Sheng, Zhengwei Ren, Yunlong Li, Xiaohan Yu, Shuangxia Jin and Jinglin Cao
Cells 2022, 11(19), 3045; https://doi.org/10.3390/cells11193045 - 28 Sep 2022
Cited by 9 | Viewed by 5240
Abstract
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous [...] Read more.
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining the dCas9 protein and transcriptional activator to achieve specific regulation of gene expression has made important contributions to biotechnology in medical research as well as agriculture. CRISPR/dCas9 activation (CRISPRa) can increase the transcription of endogenous genes. Overexpression of foreign genes by traditional transgenic technology in plant cells is the routine method to verify gene function by elevating genes transcription. One of the main limitations of the overexpression is the vector capacity constraint that makes it difficult to express multiple genes using the typical Ti plasmid vectors from Agrobacterium. The CRISPRa system can overcome these limitations of the traditional gene overexpression method and achieve multiple gene activation by simply designating several guide RNAs in one vector. This review summarizes the latest progress based on the development of CRISPRa systems, including SunTag, dCas9-VPR, dCas9-TV, scRNA, SAM, and CRISPR-Act and their applications in plants. Furthermore, limitations, challenges of current CRISPRa systems and future prospective applications are also discussed. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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11 pages, 810 KiB  
Review
Applications of CRISPR/Cas13-Based RNA Editing in Plants
by Naga Rajitha Kavuri, Manikandan Ramasamy, Yiping Qi and Kranthi Mandadi
Cells 2022, 11(17), 2665; https://doi.org/10.3390/cells11172665 - 27 Aug 2022
Cited by 15 | Viewed by 4125
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is widely used as a genome-editing tool in various organisms, including plants, to elucidate the fundamental understanding of gene function, disease diagnostics, and crop improvement. Among the CRISPR/Cas systems, Cas9 is one of [...] Read more.
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is widely used as a genome-editing tool in various organisms, including plants, to elucidate the fundamental understanding of gene function, disease diagnostics, and crop improvement. Among the CRISPR/Cas systems, Cas9 is one of the widely used nucleases for DNA modifications, but manipulation of RNA at the post-transcriptional level is limited. The recently identified type VI CRISPR/Cas systems provide a platform for precise RNA manipulation without permanent changes to the genome. Several studies reported efficient application of Cas13 in RNA studies, such as viral interference, RNA knockdown, and RNA detection in various organisms. Cas13 was also used to produce virus resistance in plants, as most plant viruses are RNA viruses. However, the application of CRISPR/Cas13 to studies of plant RNA biology is still in its infancy. This review discusses the current and prospective applications of CRISPR/Cas13-based RNA editing technologies in plants. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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Other

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12 pages, 1022 KiB  
Perspective
Analysis of the Utilization and Prospects of CRISPR-Cas Technology in the Annotation of Gene Function and Creation New Germplasm in Maize Based on Patent Data
by Youhua Wang, Qiaoling Tang, Yuli Kang, Xujing Wang, Haiwen Zhang and Xinhai Li
Cells 2022, 11(21), 3471; https://doi.org/10.3390/cells11213471 - 02 Nov 2022
Cited by 3 | Viewed by 1688
Abstract
Maize (Zea mays L.) is a food crop with the largest planting area and the highest yield in the world, and it plays a vital role in ensuring global food security. Conventional breeding methods are costly, time-consuming, and ineffective in maize breeding. [...] Read more.
Maize (Zea mays L.) is a food crop with the largest planting area and the highest yield in the world, and it plays a vital role in ensuring global food security. Conventional breeding methods are costly, time-consuming, and ineffective in maize breeding. In recent years, CRISPR-Cas editing technology has been used to quickly generate new varieties with high yield and improved grain quality and stress resistance by precisely modifying key genes involved in specific traits, thus becoming a new engine for promoting crop breeding and the competitiveness of seed industries. Using CRISPR-Cas, a range of new maize materials with high yield, improved grain quality, ideal plant type and flowering period, male sterility, and stress resistance have been created. Moreover, many patents have been filed worldwide, reflecting the huge practical application prospects and commercial value. Based on the existing patent data, we analyzed the development process, current status, and prospects of CRISPR-Cas technology in dissecting gene function and creating new germplasm in maize, providing information for future basic research and commercial production. Full article
(This article belongs to the Special Issue Plant Genome Editing: State-of-the-Art and Perspectives in China)
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