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Li R, Cui L, Martina M, Bracuto V, Meijer-Dekens F, Wolters AMA, Moglia A, Bai Y, Acquadro A. Less is more: CRISPR/Cas9-based mutations in DND1 gene enhance tomato resistance to powdery mildew with low fitness costs. BMC PLANT BIOLOGY 2024; 24:763. [PMID: 39123110 PMCID: PMC11316316 DOI: 10.1186/s12870-024-05428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
Powdery mildew (PM), triggered by Oidium neolycopersici, represents a significant threat and a major concern for the productivity of tomato plants (Solanum lycopersicum L.). The presence of susceptibility (S) genes in plants facilitates pathogen proliferation and their dysfunction can lead to a recessively inherited broad-spectrum and durable type of resistance. Past studies have demonstrated that disrupting the function of DND1 (Defense No Death 1) increases plant resilience against various pathogens, such as powdery mildew (PM), but this comes at the cost of negatively affecting the overall health and vigor of the plant. To investigate the possibility of minimizing the adverse effects of the dnd1 mutation while boosting disease resistance, a CRISPR-Cas9 construct with four single guide RNAs targeting three exons of SlDND1 (Solyc02g088560.4.1) was designed and introduced into the tomato variety Moneymaker (MM) through Agrobacterium tumefaciens-mediated transformation. Three T1 lines (named E1, E3 and E4) were crossed with MM and then selfed to produce TF2 families. All the TF2 plants in homozygous state dnd1/dnd1, showed reduced PM symptoms compared to the heterozygous (DND1/dnd1) and wild type (DND1/DND1) ones. Two full knock-out (KO) mutant events (E1 and E4) encoding truncated DND1 proteins, exhibited clear dwarfness and auto-necrosis phenotypes, while mutant event E3 harbouring deletions of 3 amino acids, showed normal growth in height with less auto-necrotic spots. Analysis of the 3D structures of both the reference and the mutant proteins revealed significant conformational alterations in the protein derived from E3, potentially impacting its function. A dnd1/dnd1 TF2 line (TV181848-9, E3) underwent whole-genome sequencing using Illumina technology, which confirmed the absence of off-target mutations in selected genomic areas. Additionally, no traces of the Cas9 gene were detected, indicating its elimination through segregation. Our findings confirm the role of DND1 as an S-gene in tomato because impairment of this gene leads to a notable reduction in susceptibility to O. neolycopersici. Moreover, we provide, for the first time, a dnd1 mutant allele (E3) that exhibits fitness advantages in comparison with previously reported dnd1 mutant alleles, indicating a possible way to breed with dnd1 mutants.
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Affiliation(s)
- Ruiling Li
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, Grugliasco, 10095, Italy
| | - Lei Cui
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
- College of Agriculture, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Matteo Martina
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, Grugliasco, 10095, Italy
| | - Valentina Bracuto
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Fien Meijer-Dekens
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Anne-Marie A Wolters
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Andrea Moglia
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, Grugliasco, 10095, Italy
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands.
| | - Alberto Acquadro
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, Grugliasco, 10095, Italy.
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Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024; 42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.
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Affiliation(s)
- Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China; Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia 46022, Spain
| | - Li Chao
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Michael G K Jones
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
| | - Hua-Feng Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia.
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Sun J, Guo J, Liu J. CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network. PLoS Comput Biol 2024; 20:e1011972. [PMID: 38483980 DOI: 10.1371/journal.pcbi.1011972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/26/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Using the CRISPR-Cas9 system to perform base substitutions at the target site is a typical technique for genome editing with the potential for applications in gene therapy and agricultural productivity. When the CRISPR-Cas9 system uses guide RNA to direct the Cas9 endonuclease to the target site, it may misdirect it to a potential off-target site, resulting in an unintended genome editing. Although several computational methods have been proposed to predict off-target effects, there is still room for improvement in the off-target effect prediction capability. In this paper, we present an effective approach called CRISPR-M with a new encoding scheme and a novel multi-view deep learning model to predict the sgRNA off-target effects for target sites containing indels and mismatches. CRISPR-M takes advantage of convolutional neural networks and bidirectional long short-term memory recurrent neural networks to construct a three-branch network towards multi-views. Compared with existing methods, CRISPR-M demonstrates significant performance advantages running on real-world datasets. Furthermore, experimental analysis of CRISPR-M under multiple metrics reveals its capability to extract features and validates its superiority on sgRNA off-target effect predictions.
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Affiliation(s)
- Jialiang Sun
- College of Computer Science, Nankai University, Tianjin, China
| | - Jun Guo
- College of Software, Northeastern University, Shenyang, China
| | - Jian Liu
- College of Computer Science, Nankai University, Tianjin, China
- Centre for Bioinformatics and Intelligent Medicine, Nankai University, Tianjin, China
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Asmamaw Mengstie M, Teshome Azezew M, Asmamaw Dejenie T, Teshome AA, Tadele Admasu F, Behaile Teklemariam A, Tilahun Mulu A, Mekonnen Agidew M, Adugna DG, Geremew H, Abebe EC. Recent Advancements in Reducing the Off-Target Effect of CRISPR-Cas9 Genome Editing. Biologics 2024; 18:21-28. [PMID: 38260716 PMCID: PMC10802171 DOI: 10.2147/btt.s429411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)) and the associated protein (Cas9) system, a young but well-studied genome-editing tool, holds plausible solutions to a wide range of genetic disorders. The single-guide RNA (sgRNA) with a 20-base user-defined spacer sequence and the Cas9 endonuclease form the core of the CRISPR-Cas9 system. This sgRNA can direct the Cas9 nuclease to any genomic region that includes a protospacer adjacent motif (PAM) just downstream and matches the spacer sequence. The current challenge in the clinical applications of CRISPR-Cas9 genome-editing technology is the potential off-target effects that can cause DNA cleavage at the incorrect sites. Off-target genome editing confuses and diminishes the therapeutic potential of CRISPR-Cas9 in addition to potentially casting doubt on scientific findings regarding the activities of genes. In this review, we summarize the recent technological advancements in reducing the off-target effect of CRISPR-Cas9 genome editing.
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Affiliation(s)
- Misganaw Asmamaw Mengstie
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Muluken Teshome Azezew
- Department of Physiology, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Assefa Agegnehu Teshome
- Department of Anatomy, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Fitalew Tadele Admasu
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Awgichew Behaile Teklemariam
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Anemut Tilahun Mulu
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Melaku Mekonnen Agidew
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Dagnew Getnet Adugna
- Department of Anatomy, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Habtamu Geremew
- College of Health Sciences, Oda Bultum University, Chiro, Ethiopia
| | - Endeshaw Chekol Abebe
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
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Li J, Kong D, Ke Y, Zeng W, Miki D. Application of multiple sgRNAs boosts efficiency of CRISPR/Cas9-mediated gene targeting in Arabidopsis. BMC Biol 2024; 22:6. [PMID: 38233866 PMCID: PMC10795408 DOI: 10.1186/s12915-024-01810-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Precise gene targeting (GT) is a powerful tool for heritable precision genome engineering, enabling knock-in or replacement of the endogenous sequence via homologous recombination. We recently established a CRISPR/Cas9-mediated approach for heritable GT in Arabidopsis thaliana (Arabidopsis) and rice and reported that the double-strand breaks (DSBs) frequency of Cas9 influences the GT efficiency. However, the relationship between DSBs and GT at the same locus was not examined. Furthermore, it has never been investigated whether an increase in the number of copies of sgRNAs or the use of multiple sgRNAs would improve the efficiency of GT. RESULTS Here, we achieved precise GT at endogenous loci Embryo Defective 2410 (EMB2410) and Repressor of Silencing 1 (ROS1) using the sequential transformation strategy and the combination of sgRNAs. We show that increasing of sgRNAs copy number elevates both DSBs and GT efficiency. On the other hand, application of multiple sgRNAs does not always enhance GT efficiency. Our results also suggested that some inefficient sgRNAs would play a role as a helper to facilitate other sgRNAs DSBs activity. CONCLUSIONS The results of this study clearly show that DSB efficiency, rather than mutation pattern, is one of the most important key factors determining GT efficiency. This study provides new insights into the relationship between sgRNAs, DSBs, and GTs and the molecular mechanisms of CRISPR/Cas9-mediated GTs in plants.
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Affiliation(s)
- Jing Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongping Ke
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Zeng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Kandasamy G, Manisekaran R, Arthikala MK. Chitosan nanoplatforms in agriculture for multi-potential applications - Adsorption/removal, sustained release, sensing of pollutants & delivering their alternatives - A comprehensive review. ENVIRONMENTAL RESEARCH 2024; 240:117447. [PMID: 37863167 DOI: 10.1016/j.envres.2023.117447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
An increase in the global population has led to an increment in the food consumption, which has demanded high food production. To meet the production demands, different techniques and technologies are adopted in agriculture the past 70 years, where utilization of the industry-manufactured/synthetic pesticides (SPTCs - e.g., herbicides, insecticides, fungicides, bactericides, nematicides, acaricides, avicides, and so on) is one of them. However, it has been later revealed that the usage of SPTCs has negatively impacted the environment - especially water and soil, and also agricultural products - mainly foods. Though preventive measures are taken by government agencies, still the utilization rate of SPTCs is high, and consequently, their maximum residual limit (MRL) levels in food are above tolerance, which further results in serious health concerns in humans. So, there is an immediate need for decreasing the utilization of the SPTCs by delivering them effectively at reduced levels in agriculture but with the required efficacy. Apart from that, it is mandatory to detect/sense and also to remove them to lessen the environmental pollution, while developing effective alternative techniques/technologies. Among many suitable materials that are developed/idenified, chitosan, a bio-polymer has gained great attention and is comprehensively implemented in all the above-mentioned applications - sensing, delivery and removal, due to their excellent and required properties. Though many works are available, in this work, a special attention is given to chitosan and its derivatives (i.e., chitosan nanoparticles (CNPs))based removal, controlled release and sensing of the SPTCs - specifically herbicides and insecticides. Moreover, the chitosan/CNPs-based protective effects on the in vivo models during/after their exposure to the SPTCs, and the current technologies like clustered regularly interspaced short palindromic repeats (CRISPR) as alternatives for SPTCs are also reviewed.
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Affiliation(s)
- Ganeshlenin Kandasamy
- Department of Biomedical Engineering, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, Tamil Nadu, India.
| | - Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures & Biomaterials, Escuela Nacional de Estudios Superiores (ENES) Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato C.P. 37689, Mexico
| | - Manoj-Kumar Arthikala
- Interdisciplinary Research Laboratory (LII), Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores (ENES) Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato C.P. 37689, Mexico
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Koller F, Cieslak M. A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment. Front Bioeng Biotechnol 2023; 11:1276226. [PMID: 37965049 PMCID: PMC10641861 DOI: 10.3389/fbioe.2023.1276226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.
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Affiliation(s)
- Franziska Koller
- Fachstelle Gentechnik und Umwelt (FGU), Munich, Bavaria, Germany
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Mackon E, Mackon GCJDE, Guo Y, Ma Y, Yao Y, Liu P. Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111746. [PMID: 37230190 DOI: 10.1016/j.plantsci.2023.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University.
| | | | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
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Mahlandt A, Singh DK, Mercier R. Engineering apomixis in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:131. [PMID: 37199785 DOI: 10.1007/s00122-023-04357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/04/2023] [Indexed: 05/19/2023]
Abstract
Apomixis is an asexual mode of reproduction through seeds where progeny are clones of the mother plants. Naturally apomictic modes of reproduction are found in hundreds of plant genera distributed across more than 30 plant families, but are absent in major crop plants. Apomixis has the potential to be a breakthrough technology by allowing the propagation through seed of any genotype, including F1 hybrids. Here, we have summarized the recent progress toward synthetic apomixis, where combining targeted modifications of both the meiosis and fertilization processes leads to the production of clonal seeds at high frequencies. Despite some remaining challenges, the technology has approached a level of maturity that allows its consideration for application in the field.
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Affiliation(s)
- Alexander Mahlandt
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Dipesh Kumar Singh
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany.
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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12
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The rising threat of geminiviruses: molecular insights into the disease mechanism and mitigation strategies. Mol Biol Rep 2023; 50:3835-3848. [PMID: 36701042 DOI: 10.1007/s11033-023-08266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Geminiviruses are among the most threatening emerging plant viruses, accountable for a huge loss to agricultural production worldwide. These viruses have been responsible for some serious outbreaks during the last few decades across different parts of the world. Sincere efforts have been made to regulate the disease incidence by incorporating a multi-dimensional approach, and this process has been facilitated greatly by the advent of molecular techniques. But, the mixed infection due to the polyphagous nature of vectors results in viral recombination followed by the emergence of novel viral strains which thus renders the existing mitigation strategies ineffective. Hence, a multifaceted insight into the molecular mechanism of the disease is really needed to understand the regulatory points; much has been done in this direction during the last few years. The present review aims to explore all the latest developments made so far and to organize the information in a comprehensive manner so that some novel hypotheses for controlling the disease may be generated. METHODS AND RESULTS Starting with the background information, diverse genera of geminiviruses are listed along with their pathological and economic impacts. A comprehensive and detailed mechanism of infection is elaborated to study the interactions between vector, host, and virus at different stages in the life cycle of geminiviruses. Finally, an effort isalso made to analyze the progress made at the molecular level for the development of various mitigation strategies and suggest more effective and better approaches for controlling the disease. CONCLUSION The study has provided a thorough understanding of molecular mechanism of geminivirus infection.
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13
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Nikolić I, Samardžić J, Stevanović S, Miljuš-Đukić J, Milisavljević M, Timotijević G. CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. Int J Mol Sci 2023; 24:ijms24032442. [PMID: 36768765 PMCID: PMC9916663 DOI: 10.3390/ijms24032442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/28/2023] Open
Abstract
Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response.
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14
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Morales KY, Bridgeland AH, Hake KD, Udall JA, Thomson MJ, Yu JZ. Homology-based identification of candidate genes for male sterility editing in upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1006264. [PMID: 36589117 PMCID: PMC9795482 DOI: 10.3389/fpls.2022.1006264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) accounts for more than 90% of the world's cotton production, providing natural material for the textile and oilseed industries worldwide. One strategy for improving upland cotton yields is through increased adoption of hybrids; however, emasculation of cotton flowers is incredibly time-consuming and genetic sources of cotton male sterility are limited. Here we review the known biochemical modes of plant nuclear male sterility (NMS), often known as plant genetic male sterility (GMS), and characterized them into four groups: transcriptional regulation, splicing, fatty acid transport and processing, and sugar transport and processing. We have explored protein sequence homology from 30 GMS genes of three monocots (maize, rice, and wheat) and three dicots (Arabidopsis, soybean, and tomato). We have analyzed evolutionary relationships between monocot and dicot GMS genes to describe the relative similarity and relatedness of these genes identified. Five were lowly conserved to their source species, four unique to monocots, five unique to dicots, 14 highly conserved among all species, and two in the other category. Using this source, we have identified 23 potential candidate genes within the upland cotton genome for the development of new male sterile germplasm to be used in hybrid cotton breeding. Combining homology-based studies with genome editing may allow for the discovery and validation of GMS genes that previously had no diversity observed in cotton and may allow for development of a desirable male sterile mutant to be used in hybrid cotton production.
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Affiliation(s)
- Karina Y. Morales
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Aya H. Bridgeland
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Kater D. Hake
- Cotton Incorporated, Agricultural and Environment Research, Cary, NC, United States
| | - Joshua A. Udall
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
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15
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Valeeva LR, Dzhabrailova SM, Sharipova MR. cis-Prenyltransferases of Marchantia polymorpha: Phylogenetic Analysis and Perspectives for Use as Regulators of Antimicrobial Agent Synthesis. Mol Biol 2022. [DOI: 10.1134/s002689332206019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Li R, Maioli A, Yan Z, Bai Y, Valentino D, Milani AM, Pompili V, Comino C, Lanteri S, Moglia A, Acquadro A. CRISPR/Cas9-Based Knock-Out of the PMR4 Gene Reduces Susceptibility to Late Blight in Two Tomato Cultivars. Int J Mol Sci 2022; 23:ijms232314542. [PMID: 36498869 PMCID: PMC9735651 DOI: 10.3390/ijms232314542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Phytophthora infestans, the causal agent of late blight (LB) in tomato (Solanum lycopersicum L.), is a devastating disease and a serious concern for plant productivity. The presence of susceptibility (S) genes in plants facilitates pathogen proliferation; thus, disabling these genes may help provide a broad-spectrum and durable type of tolerance/resistance. Previous studies on Arabidopsis and tomato have highlighted that knock-out mutants of the PMR4 susceptibility gene are tolerant to powdery mildew. Moreover, PMR4 knock-down in potato has been shown to confer tolerance to LB. To verify the same effect in tomato in the present study, a CRISPR-Cas9 vector containing four single guide RNAs (sgRNAs: sgRNA1, sgRNA6, sgRNA7, and sgRNA8), targeting as many SlPMR4 regions, was introduced via Agrobacterium-tumefaciens-mediated transformation into two widely grown Italian tomato cultivars: 'San Marzano' (SM) and 'Oxheart' (OX). Thirty-five plants (twenty-six SM and nine OX) were selected and screened to identify the CRISPR/Cas9-induced mutations. The different sgRNAs caused mutation frequencies ranging from 22.1 to 100% and alternatively precise insertions (sgRNA6) or deletions (sgRNA7, sgRNA1, and sgRNA8). Notably, sgRNA7 induced in seven SM genotypes a -7 bp deletion in the homozygous status, whereas sgRNA8 led to the production of fifteen SM genotypes with a biallelic mutation (-7 bp and -2 bp). Selected edited lines were inoculated with P. infestans, and four of them, fully knocked out at the PMR4 locus, showed reduced disease symptoms (reduction in susceptibility from 55 to 80%) compared to control plants. The four SM lines were sequenced using Illumina whole-genome sequencing for deeper characterization without exhibiting any evidence of mutations in the candidate off-target regions. Our results showed, for the first time, a reduced susceptibility to Phytophtora infestans in pmr4 tomato mutants confirming the role of KO PMR4 in providing broad-spectrum protection against pathogens.
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Affiliation(s)
- Ruiling Li
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Alex Maioli
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Zhe Yan
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Danila Valentino
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Anna Maria Milani
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Valerio Pompili
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Cinzia Comino
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Sergio Lanteri
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Andrea Moglia
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Alberto Acquadro
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
- Correspondence:
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17
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Robertson G, Burger J, Campa M. CRISPR/Cas-based tools for the targeted control of plant viruses. MOLECULAR PLANT PATHOLOGY 2022; 23:1701-1718. [PMID: 35920132 PMCID: PMC9562834 DOI: 10.1111/mpp.13252] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 05/15/2023]
Abstract
Plant viruses are known to infect most economically important crops and pose a major threat to global food security. Currently, few resistant host phenotypes have been delineated, and while chemicals are used for crop protection against insect pests and bacterial or fungal diseases, these are inefficient against viral diseases. Genetic engineering emerged as a way of modifying the plant genome by introducing functional genes in plants to improve crop productivity under adverse environmental conditions. Recently, new breeding technologies, and in particular the exciting CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) technology, was shown to be a powerful alternative to engineer resistance against plant viruses, thus has great potential for reducing crop losses and improving plant productivity to directly contribute to food security. Indeed, it could circumvent the "Genetic modification" issues because it allows for genome editing without the integration of foreign DNA or RNA into the genome of the host plant, and it is simpler and more versatile than other new breeding technologies. In this review, we describe the predominant features of the major CRISPR/Cas systems and outline strategies for the delivery of CRISPR/Cas reagents to plant cells. We also provide an overview of recent advances that have engineered CRISPR/Cas-based resistance against DNA and RNA viruses in plants through the targeted manipulation of either the viral genome or susceptibility factors of the host plant genome. Finally, we provide insight into the limitations and challenges that CRISPR/Cas technology currently faces and discuss a few alternative applications of the technology in virus research.
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Affiliation(s)
- Gaëlle Robertson
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
- Department of Experimental and Health SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Johan Burger
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
| | - Manuela Campa
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
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18
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Kumari D, Prasad BD, Dwivedi P, Hidangmayum A, Sahni S. CRISPR/Cas9 mediated genome editing tools and their possible role in disease resistance mechanism. Mol Biol Rep 2022; 49:11587-11600. [DOI: 10.1007/s11033-022-07851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
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19
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Garland S, Curry HA. Turning promise into practice: Crop biotechnology for increasing genetic diversity and climate resilience. PLoS Biol 2022; 20:e3001716. [PMID: 35881573 PMCID: PMC9321377 DOI: 10.1371/journal.pbio.3001716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
As climate change increasingly threatens agricultural production, expanding genetic diversity in crops is an important strategy for climate resilience in many agricultural contexts. In this Essay, we explore the potential of crop biotechnology to contribute to this diversification, especially in industrialized systems, by using historical perspectives to frame the current dialogue surrounding recent innovations in gene editing. We unearth comments about the possibility of enhancing crop diversity made by ambitious scientists in the early days of recombinant DNA and follow the implementation of this technology, which has not generated the diversification some anticipated. We then turn to recent claims about the promise of gene editing tools with respect to this same goal. We encourage researchers and other stakeholders to engage in activities beyond the laboratory if they hope to see what is technologically possible translated into practice at this critical point in agricultural transformation.
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Affiliation(s)
- Sarah Garland
- The Earth Institute, Columbia University, New York, New York, United States of America
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Cambridge, United Kingdom
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20
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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21
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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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22
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Sturme MHJ, van der Berg JP, Bouwman LMS, De Schrijver A, de Maagd RA, Kleter GA, Battaglia-de Wilde E. Occurrence and Nature of Off-Target Modifications by CRISPR-Cas Genome Editing in Plants. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2022; 2:192-201. [PMID: 35548699 PMCID: PMC9075866 DOI: 10.1021/acsagscitech.1c00270] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022]
Abstract
![]()
CRISPR-Cas-based
genome editing allows for precise and targeted
genetic modification of plants. Nevertheless, unintended off-target
edits can arise that might confer risks when present in gene-edited
food crops. Through an extensive literature review we gathered information
on CRISPR-Cas off-target edits in plants. Most observed off-target
changes were small insertions or deletions (1–22 bp) or nucleotide
substitutions, and large deletions (>100 bp) were rare. One study
detected the insertion of vector-derived DNA sequences, which is important
considering the risk assessment of gene-edited plants. Off-target
sites had few mismatches (1–3 nt) with the target sequence
and were mainly located in protein-coding regions, often in target
gene homologues. Off-targets edits were predominantly detected via
biased analysis of predicted off-target sites instead of unbiased
genome-wide analysis. CRISPR-Cas-edited plants showed lower off-target
mutation frequencies than conventionally bred plants. This Review
can aid discussions on the relevance of evaluating off-target modifications
for risk assessment of CRISPR-Cas-edited plants.
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Affiliation(s)
- Mark H J Sturme
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Jan Pieter van der Berg
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Lianne M S Bouwman
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Ruud A de Maagd
- Wageningen Plant Research, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Gijs A Kleter
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Evy Battaglia-de Wilde
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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23
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Impens L, Jacobs TB, Nelissen H, Inzé D, Pauwels L. Mini-Review: Transgenerational CRISPR/Cas9 Gene Editing in Plants. Front Genome Ed 2022; 4:825042. [PMID: 35187531 PMCID: PMC8854858 DOI: 10.3389/fgeed.2022.825042] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9 genome editing has been used extensively in a wide variety of plant species. Creation of loss-of-function alleles, promoter variants and mutant collections are a few of the many uses of genome editing. In a typical workflow for sexually reproducing species, plants are generated that contain an integrated CRISPR/Cas9 transgene. After editing of the gene of interest, T-DNA null segregants can be identified in the next generation that contain only the desired edit. However, maintained presence of the CRISPR/Cas9 transgene and continued editing in the subsequent generations offer a range of applications for model plants and crops. In this review, we define transgenerational gene editing (TGE) as the continued editing of CRISPR/Cas9 after a genetic cross. We discuss the concept of TGE, summarize the current main applications, and highlight special cases to illustrate the importance of TGE for plant genome editing research and breeding.
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Affiliation(s)
- Lennert Impens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas B. Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Laurens Pauwels,
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24
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Roy RK, Debashree I, Srivastava S, Rishi N, Srivastava A. CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction,
Detection, and Overcoming Strategies. Curr Bioinform 2022. [DOI: 10.2174/1574893616666210708150439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
CRISPR/Cas9 technology is a highly flexible RNA-guided endonuclease (RGEN)
based gene-editing tool that has transformed the field of genomics, gene therapy, and genome/
epigenome imaging. Its wide range of applications provides immense scope for understanding
as well as manipulating genetic/epigenetic elements. However, the RGEN is prone to
off-target mutagenesis that leads to deleterious effects. This review details the molecular and cellular
mechanisms underlying the off-target activity, various available detection tools and prediction
methodology ranging from sequencing to machine learning approaches, and the strategies to
overcome/minimise off-targets. A coherent and concise method increasing target precision would
prove indispensable to concrete manipulation and interpretation of genome editing results that
can revolutionise therapeutics, including clarity in genome regulatory mechanisms during development.
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Affiliation(s)
- Roshan Kumar Roy
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313, India
| | - Ipsita Debashree
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313, India
| | - Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
| | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
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Hüdig M, Laibach N, Hein AC. Genome Editing in Crop Plant Research-Alignment of Expectations and Current Developments. PLANTS (BASEL, SWITZERLAND) 2022; 11:212. [PMID: 35050100 PMCID: PMC8778883 DOI: 10.3390/plants11020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
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 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.
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Affiliation(s)
- Meike Hüdig
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Natalie Laibach
- Centre for Research in Agricultural Genomics (CRAG), Edifici CRAG-Campus UAB, 08193 Cerdanyola del Vallès, Spain
| | - Anke-Christiane Hein
- Federal Agency for Nature Conservation, Assessment of Genetically Modified Organisms, Konstantinstraße 110, 53179 Bonn, Germany
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Gianoglio S, Comino C, Moglia A, Acquadro A, García-Carpintero V, Diretto G, Sevi F, Rambla JL, Dono G, Valentino D, Moreno-Giménez E, Fullana-Pericàs M, Conesa MA, Galmés J, Lanteri S, Mazzucato A, Orzáez D, Granell A. In-Depth Characterization of greenflesh Tomato Mutants Obtained by CRISPR/Cas9 Editing: A Case Study With Implications for Breeding and Regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:936089. [PMID: 35898224 PMCID: PMC9309892 DOI: 10.3389/fpls.2022.936089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Gene editing has already proved itself as an invaluable tool for the generation of mutants for crop breeding, yet its ultimate impact on agriculture will depend on how crops generated by gene editing technologies are regulated, and on our ability to characterize the impact of mutations on plant phenotype. A starting operational strategy for evaluating gene editing-based approaches to plant breeding might consist of assessing the effect of the induced mutations in a crop- and locus-specific manner: this involves the analysis of editing efficiency in different cultivars of a crop, the assessment of potential off-target mutations, and a phenotypic evaluation of edited lines carrying different mutated alleles. Here, we targeted the GREENFLESH (GF) locus in two tomato cultivars ('MoneyMaker' and 'San Marzano') and evaluated the efficiency, specificity and mutation patterns associated with CRISPR/Cas9 activity for this gene. The GF locus encodes a Mg-dechelatase responsible for initiating chlorophyll degradation; in gf mutants, ripe fruits accumulate both carotenoids and chlorophylls. Phenotypic evaluations were conducted on two transgene-free T2 'MoneyMaker' gf lines with different mutant alleles (a small insertion of 1 nucleotide and a larger deletion of 123 bp). Both lines, in addition to reduced chlorophyll degradation, showed a notable increase in carotenoid and tocopherol levels during fruit ripening. Infection of gf leaves and fruits with Botrytis cinerea resulted in a significant reduction of infected area and pathogen proliferation compared to the wild type (WT). Our data indicates that the CRISPR/Cas9-mediated mutation of the GF locus in tomato is efficient, specific and reproducible and that the resulting phenotype is robust and consistent with previously characterized greenflesh mutants obtained with different breeding techniques, while also shedding light on novel traits such as vitamin E overaccumulation and pathogen resistance. This makes GF an appealing target for breeding tomato cultivars with improved features for cultivation, as well as consumer appreciation and health.
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Affiliation(s)
- Silvia Gianoglio
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Víctor García-Carpintero
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Rome, Italy
| | - Filippo Sevi
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Rome, Italy
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - José Luis Rambla
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Gabriella Dono
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Danila Valentino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Elena Moreno-Giménez
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA-CSIC), Paterna, Spain
| | - Mateu Fullana-Pericàs
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA), Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, Palma, Spain
| | - Miguel A. Conesa
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA), Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, Palma, Spain
| | - Jeroni Galmés
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA), Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, Palma, Spain
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Diego Orzáez
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
| | - Antonio Granell
- Departamento de Biotecnología de Cultivos, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) – Universitat Politécnica de Valéncia (UPV), Valencia, Spain
- *Correspondence: Antonio Granell,
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Mohan C, Easterling M, Yau YY. Gene Editing Technologies for Sugarcane Improvement: Opportunities and Limitations. SUGAR TECH : AN INTERNATIONAL JOURNAL OF SUGAR CROPS & RELATED INDUSTRIES 2022; 24:369-385. [PMID: 34667393 PMCID: PMC8517945 DOI: 10.1007/s12355-021-01045-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/07/2021] [Indexed: 05/05/2023]
Abstract
Plant-based biofuels present a promising alternative to depleting non-renewable fuel resources. One of the benefits of biofuel is reduced environmental impact, including reduction in greenhouse gas emission which causes climate change. Sugarcane is one of the most important bioenergy crops. Sugarcane juice is used to produce table sugar and first-generation biofuel (e.g., bioethanol). Sugarcane bagasse is also a potential material for second-generation cellulosic biofuel production. Researchers worldwide are striving to improve sugarcane biomass yield and quality by a variety of means including biotechnological tools. This paper reviews the use of sugarcane as a feedstock for biofuel production, and gene manipulation tools and approaches, including RNAi and genome-editing tools, such as TALENs and CRISPR-Cas9, for improving its quality. The specific focus here is on CRISPR system because it is low cost, simple in design and versatile compared to other genome-editing tools. The advance of CRISPR-Cas9 technology has transformed plant research with its ability to precisely delete, insert or replace genes in recent years. Lignin is the primary material responsible for biomass recalcitrance in biofuel production. The use of genome editing technology to modify lignin composition and distribution in sugarcane cell wall has been realized. The current and potential applications of genome editing technology for sugarcane improvement are discussed. The advantages and limitations of utilizing RNAi and TALEN techniques in sugarcane improvement are discussed as well.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mona Easterling
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
- Northeast Campus, Tulsa Community College, 3727 East Apache St, Tulsa, OK 74115 USA
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
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28
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Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
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Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
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29
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Klimek-Chodacka M, Gieniec M, Baranski R. Multiplex Site-Directed Gene Editing Using Polyethylene Glycol-Mediated Delivery of CRISPR gRNA:Cas9 Ribonucleoprotein (RNP) Complexes to Carrot Protoplasts. Int J Mol Sci 2021; 22:10740. [PMID: 34639081 PMCID: PMC8509836 DOI: 10.3390/ijms221910740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/03/2021] [Indexed: 01/25/2023] Open
Abstract
The aim of this work was to show an efficient, recombinant DNA-free, multiplex gene-editing method using gRNA:Cas9 ribonucleoprotein (RNP) complexes delivered directly to plant protoplasts. For this purpose, three RNPs were formed in the tube, their activity was confirmed by DNA cleavage in vitro, and then they were delivered to carrot protoplasts incubated with polyethylene glycol (PEG). After 48 h of incubation, single nucleotide deletions and insertions and small deletions at target DNA sites were identified by using fluorescent-PCR capillary electrophoresis and sequencing. When two or three RNPs were delivered simultaneously, long deletions of 33-152 nt between the gRNA target sites were generated. Such mutations occurred with an efficiency of up to 12%, while the overall editing effectiveness was very high, reaching 71%. This highly efficient multiplex gene-editing method, without the need for recombinant DNA technology, can be adapted to other plants for which protoplast culture methods have been established.
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Affiliation(s)
- Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
| | | | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
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30
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Venezia M, Creasey Krainer KM. Current Advancements and Limitations of Gene Editing in Orphan Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:742932. [PMID: 34630494 PMCID: PMC8493294 DOI: 10.3389/fpls.2021.742932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 05/23/2023]
Abstract
Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.
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31
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Khusnutdinov E, Sukhareva A, Panfilova M, Mikhaylova E. Anthocyanin Biosynthesis Genes as Model Genes for Genome Editing in Plants. Int J Mol Sci 2021; 22:8752. [PMID: 34445458 PMCID: PMC8395717 DOI: 10.3390/ijms22168752] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas, one of the most rapidly developing technologies in the world, has been applied successfully in plant science. To test new nucleases, gRNA expression systems and other inventions in this field, several plant genes with visible phenotypic effects have been constantly used as targets. Anthocyanin pigmentation is one of the most easily identified traits, that does not require any additional treatment. It is also associated with stress resistance, therefore plants with edited anthocyanin genes might be of interest for agriculture. Phenotypic effect of CRISPR/Cas editing of PAP1 and its homologs, DFR, F3H and F3'H genes have been confirmed in several distinct plant species. DFR appears to be a key structural gene of anthocyanin biosynthesis, controlled by various transcription factors. There are still many promising potential model genes that have not been edited yet. Some of them, such as Delila, MYB60, HAT1, UGT79B2, UGT79B3 and miR156, have been shown to regulate drought tolerance in addition to anthocyanin biosynthesis. Genes, also involved in trichome development, such as TTG1, GLABRA2, MYBL2 and CPC, can provide increased visibility. In this review successful events of CRISPR/Cas editing of anthocyanin genes are summarized, and new model genes are proposed. It can be useful for molecular biologists and genetic engineers, crop scientists, plant genetics and physiologists.
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Affiliation(s)
| | | | | | - Elena Mikhaylova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia; (E.K.); (A.S.); (M.P.)
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32
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Confalonieri M, Carelli M, Gianoglio S, Moglia A, Biazzi E, Tava A. CRISPR/Cas9-Mediated Targeted Mutagenesis of CYP93E2 Modulates the Triterpene Saponin Biosynthesis in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:690231. [PMID: 34381478 PMCID: PMC8350446 DOI: 10.3389/fpls.2021.690231] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
In the Medicago genus, triterpene saponins are a group of bioactive compounds extensively studied for their different biological and pharmaceutical properties. In this work, the CRISPR/Cas9-based approach with two single-site guide RNAs was used in Medicago truncatula (barrel medic) to knock-out the CYP93E2 and CYP72A61 genes, which are responsible for the biosynthesis of soyasapogenol B, the most abundant soyasapogenol in Medicago spp. No transgenic plants carrying mutations in the target CYP72A61 gene were recovered while fifty-two putative CYP93E2 mutant plant lines were obtained following Agrobacterium tumefaciens-mediated transformation. Among these, the fifty-one sequenced plant lines give an editing efficiency of 84%. Sequencing revealed that these lines had various mutation patterns at the target sites. Four T0 mutant plant lines were further selected and examined for their sapogenin content and plant growth performance under greenhouse conditions. The results showed that all tested CYP93E2 knock-out mutants did not produce soyasapogenols in the leaves, stems and roots, and diverted the metabolic flux toward the production of valuable hemolytic sapogenins. No adverse influence was observed on the plant morphological features of CYP93E2 mutants under greenhouse conditions. In addition, differential expression of saponin pathway genes was observed in CYP93E2 mutants in comparison to the control. Our results provide new and interesting insights into the application of CRISPR/Cas9 for metabolic engineering of high-value compounds of plant origin and will be useful to investigate the physiological functions of saponins in planta.
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Affiliation(s)
- Massimo Confalonieri
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Maria Carelli
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Elisa Biazzi
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Aldo Tava
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Lodi, Italy
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33
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Karki U, Fang H, Guo W, Unnold-Cofre C, Xu J. Cellular engineering of plant cells for improved therapeutic protein production. PLANT CELL REPORTS 2021; 40:1087-1099. [PMID: 33837823 PMCID: PMC8035600 DOI: 10.1007/s00299-021-02693-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/29/2021] [Indexed: 05/07/2023]
Abstract
In vitro cultured plant cells, in particular the tobacco BY-2 cell, have demonstrated their potential to provide a promising bioproduction platform for therapeutic proteins by integrating the merits of whole-plant cultivation systems with those of microbial and mammalian cell cultures. Over the past three decades, substantial progress has been made in improving the plant cell culture system, resulting in a few commercial success cases, such as taliglucerase alfa (Elelyso®), the first FDA-approved recombinant pharmaceutical protein derived from plant cells. However, compared to the major expression hosts (bacteria, yeast, and mammalian cells), plant cells are still largely underutilized, mainly due to low productivity and non-human glycosylation. Modern molecular biology tools, in particular RNAi and the latest genome editing technology CRISPR/Cas9, have been used to modulate the genome of plant cells to create new cell lines that exhibit desired "traits" for producing therapeutic proteins. This review highlights the recent advances in cellular engineering of plant cells towards improved recombinant protein production, including creating cell lines with deficient protease levels or humanized glycosylation, and considers potential development in the future.
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Affiliation(s)
- Uddhab Karki
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Hong Fang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- College of Agriculture, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Wenzheng Guo
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Carmela Unnold-Cofre
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Jianfeng Xu
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA.
- College of Agriculture, Arkansas State University, Jonesboro, AR, 72401, USA.
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Abstract
In keeping with the directive in Executive Order 13874 (Modernizing the Regulatory Framework for Agricultural Biotechnology Products) to adopt regulatory approaches that are proportionate to risk and avoid arbitrary distinctions across like products, the US Department of Agriculture (USDA) revised its biotechnology regulations by promulgating the Sustainable, Ecological, Consistent, Uniform, Responsible, and Efficient (SECURE) rule. Specifically, the SECURE rule 1) establishes exemptions for plants modified by genetic engineering where the modification could otherwise have been made through conventional breeding, 2) uses risk posed by the introduced trait to determine whether an organism is regulated, rather than relying on whether the organism was developed using a plant pest, and 3) provides a mechanism for a rapid initial review to efficiently distinguish plants developed using genetic engineering that do not pose plausible pathways to increased plant pest risk from those that do. As a result of the focused oversight on potentially riskier crops developed using genetic engineering, USDA is expected to improve the efficiency and effectiveness of its oversight program. The reduced regulatory burden is expected to promote innovation by expanding the number and diversity of developers to include smaller businesses and academics and to increase the number and variety of traits being developed through biotechnology.
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Affiliation(s)
- Neil E Hoffman
- Biotechnology Regulatory Services, Animal Plant Health Inspection Services, US Department of Agriculture, Riverdale, MD 20737
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35
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Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S, Ma W, She M. Application of CRISPR/Cas9 in Crop Quality Improvement. Int J Mol Sci 2021; 22:4206. [PMID: 33921600 PMCID: PMC8073294 DOI: 10.3390/ijms22084206] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.
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Affiliation(s)
- Qier Liu
- Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Fan Yang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Hang Liu
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shanjida Rahman
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Maoyun She
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
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Kumar S, Rymarquis LA, Ezura H, Nekrasov V. Editorial: CRISPR-Cas in Agriculture: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2021; 12:672329. [PMID: 33841487 PMCID: PMC8034289 DOI: 10.3389/fpls.2021.672329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 05/29/2023]
Affiliation(s)
| | | | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden, United Kingdom
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Tyagi S, Kumar R, Kumar V, Won SY, Shukla P. Engineering disease resistant plants through CRISPR-Cas9 technology. GM CROPS & FOOD 2021; 12:125-144. [PMID: 33079628 PMCID: PMC7583490 DOI: 10.1080/21645698.2020.1831729] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/13/2020] [Accepted: 09/27/2020] [Indexed: 01/08/2023]
Abstract
Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.
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Affiliation(s)
- Swati Tyagi
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Robin Kumar
- Department of Soil Science and Agricultural Chemistry, Acharya Narendra Dev University of Agriculture and Technology, Kumarganj, Ayodhya, India
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - Vivak Kumar
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - So Youn Won
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Donovan S, Mao Y, Orr DJ, Carmo-Silva E, McCormick AJ. CRISPR-Cas9-Mediated Mutagenesis of the Rubisco Small Subunit Family in Nicotiana tabacum. Front Genome Ed 2020; 2:605614. [PMID: 34713229 PMCID: PMC8525408 DOI: 10.3389/fgeed.2020.605614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Engineering the small subunit of the key CO2-fixing enzyme Rubisco (SSU, encoded by rbcS) in plants currently poses a significant challenge, as many plants have polyploid genomes and SSUs are encoded by large multigene families. Here, we used CRISPR-Cas9-mediated genome editing approach to simultaneously knock-out multiple rbcS homologs in the model tetraploid crop tobacco (Nicotiana tabacum cv. Petit Havana). The three rbcS homologs rbcS_S1a, rbcS_S1b and rbcS_T1 account for at least 80% of total rbcS expression in tobacco. In this study, two multiplexing guide RNAs (gRNAs) were designed to target homologous regions in these three genes. We generated tobacco mutant lines with indel mutations in all three genes, including one line with a 670 bp deletion in rbcS-T1. The Rubisco content of three selected mutant lines in the T1 generation was reduced by ca. 93% and mutant plants accumulated only 10% of the total biomass of wild-type plants. As a second goal, we developed a proof-of-principle approach to simultaneously introduce a non-native rbcS gene while generating the triple SSU knockout by co-transformation into a wild-type tobacco background. Our results show that CRISPR-Cas9 is a viable tool for the targeted mutagenesis of rbcS families in polyploid species and will contribute to efforts aimed at improving photosynthetic efficiency through expression of superior non-native Rubisco enzymes in plants.
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Affiliation(s)
- Sophie Donovan
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yuwei Mao
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Milner MJ, Craze M, Hope MS, Wallington EJ. Turning Up the Temperature on CRISPR: Increased Temperature Can Improve the Editing Efficiency of Wheat Using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2020; 11:583374. [PMID: 33324433 PMCID: PMC7726164 DOI: 10.3389/fpls.2020.583374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/23/2020] [Indexed: 05/24/2023]
Abstract
The application of CRISPR/Cas9 technologies has transformed our ability to target and edit designated regions of a genome. It's broad adaptability to any organism has led to countless advancements in our understanding of many biological processes. Many current tools are designed for simple plant systems such as diploid species, however, efficient deployment in crop species requires a greater efficiency of editing as these often contain polyploid genomes. Here, we examined the role of temperature to understand if CRISPR/Cas9 editing efficiency can be improved in wheat. The recent finding that plant growth under higher temperatures could increase mutation rates was tested with Cas9 expressed from two different promoters in wheat. Increasing the temperature of the tissue culture or of the seed germination and early growth phase increases the frequency of mutation in wheat when the Cas9 enzyme is driven by the ZmUbi promoter but not OsActin. In contrast, Cas9 expression driven by the OsActin promoter did not increase the mutations detected in either transformed lines or during the transformation process itself. These results demonstrate that CRISPR/Cas9 editing efficiency can be significantly increased in a polyploid cereal species with a simple change in growth conditions to facilitate increased mutations for the creation of homozygous or null knock-outs.
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Modrzejewski D, Hartung F, Lehnert H, Sprink T, Kohl C, Keilwagen J, Wilhelm R. Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:574959. [PMID: 33329634 PMCID: PMC7719684 DOI: 10.3389/fpls.2020.574959] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/30/2020] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas enables a targeted modification of DNA sequences. Despite their ease and efficient use, one limitation is the potential occurrence of associated off-target effects. This systematic review aims to answer the following research question: Which factors affect the occurrence of off-target effects caused by the use of CRISPR/Cas in plants? Literature published until March 2019 was considered for this review. Articles were screened for relevance based on pre-defined inclusion criteria. Relevant studies were subject to critical appraisal. All studies included in the systematic review were synthesized in a narrative report, but studies rated as high and medium/high validity were reported separately from studies rated as low and medium/low or unclear validity. In addition, we ran a binary logistic regression analysis to verify five factors that may affect the occurrence of off-target effects: (1) Number of mismatches (2) Position of mismatches (3) GC-content of the targeting sequence (4) Altered nuclease variants (5) Delivery methods. In total, 180 relevant articles were included in this review containing 468 studies therein. Seventy nine percentage of these studies were rated as having high or medium/high validity. Within these studies, 6,416 potential off-target sequences were assessed for the occurrence of off-target effects. Results clearly indicate that an increased number of mismatches between the on-target and potential off-target sequence steeply decreases the likelihood of off-target effects. The observed rate of off-target effects decreased from 59% when there is one mismatch between the on-target and off-target sequences toward 0% when four or more mismatches exist. In addition, mismatch/es located within the first eight nucleotides proximal to the PAM significantly decreased the occurrence of off-target effects. There is no evidence that the GC-content significantly affects off-target effects. The database regarding the impact of the nuclease variant and the delivery method is very poor as the majority of studies applied the standard nuclease SpCas9 and the CRISPR/Cas system was stably delivered in the genome. Hence, a general significant impact of these two factors on the occurrence of off-target effects cannot be proved. This identified evidence gap needs to be filled by systematic studies exploring these individual factors in sufficient numbers.
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Affiliation(s)
- Dominik Modrzejewski
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
| | - Frank Hartung
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
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Naegeli H, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Mullins E, Nogué F, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Casacuberta J, Gennaro A, Paraskevopoulos K, Raffaello T, Rostoks N. Applicability of the EFSA Opinion on site-directed nucleases type 3 for the safety assessment of plants developed using site-directed nucleases type 1 and 2 and oligonucleotide-directed mutagenesis. EFSA J 2020; 18:e06299. [PMID: 33281977 PMCID: PMC7684970 DOI: 10.2903/j.efsa.2020.6299] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The European Commission requested the EFSA Panel on Genetically Modified Organisms (GMO) to assess whether section 4 (hazard identification) and the conclusions of EFSA's Scientific opinion on the risk assessment of plants developed using zinc finger nuclease type 3 technique (ZFN-3) and other site-directed nucleases (SDN) with similar function are valid for plants developed via SDN-1, SDN-2 and oligonucleotide-directed mutagenesis (ODM). In delivering this Opinion, the GMO Panel compared the hazards associated with plants produced via SDN-1, SDN-2 and ODM with those associated with plants obtained via both SDN-3 and conventional breeding. Unlike for SDN-3 methods, the application of SDN-1, SDN-2 and ODM approaches aims to modify genomic sequences in a way which can result in plants not containing any transgene, intragene or cisgene. Consequently, the GMO Panel concludes that those considerations which are specifically related to the presence of a transgene, intragene or cisgene included in section 4 and the conclusions of the Opinion on SDN-3 are not relevant to plants obtained via SDN-1, SDN-2 or ODM as defined in this Opinion. Overall, the GMO Panel did not identify new hazards specifically linked to the genomic modification produced via SDN-1, SDN-2 or ODM as compared with both SDN-3 and conventional breeding. Furthermore, the GMO Panel considers that the existing Guidance for risk assessment of food and feed from genetically modified plants and the Guidance on the environmental risk assessment of genetically modified plants are sufficient but are only partially applicable to plants generated via SDN-1, SDN-2 or ODM. Indeed, those guidance documents' requirements that are linked to the presence of exogenous DNA are not relevant for the risk assessment of plants developed via SDN-1, SDN-2 or ODM approaches if the genome of the final product does not contain exogenous DNA.
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Xu H, Zhang L, Zhang K, Ran Y. Progresses, Challenges, and Prospects of Genome Editing in Soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2020; 11:571138. [PMID: 33193504 PMCID: PMC7642200 DOI: 10.3389/fpls.2020.571138] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/28/2020] [Indexed: 05/17/2023]
Abstract
Soybean is grown worldwide for oil and protein source as food, feed and industrial raw material for biofuel. Steady increase in soybean production in the past century mainly attributes to genetic mediation including hybridization, mutagenesis and transgenesis. However, genetic resource limitation and intricate social issues in use of transgenic technology impede soybean improvement to meet rapid increases in global demand for soybean products. New approaches in genomics and development of site-specific nucleases (SSNs) based genome editing technologies have expanded soybean genetic variations in its germplasm and have potential to make precise modification of genes controlling the important agronomic traits in an elite background. ZFNs, TALENS and CRISPR/Cas9 have been adapted in soybean improvement for targeted deletions, additions, replacements and corrections in the genome. The availability of reference genome assembly and genomic resources increases feasibility in using current genome editing technologies and their new development. This review summarizes the status of genome editing in soybean improvement and future directions in this field.
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Affiliation(s)
| | | | | | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
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Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5963-5975. [PMID: 32734287 DOI: 10.1093/jxb/eraa316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] and T-DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (~3% relative to the wild-type) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests that this is a viable approach for exploring the functional roles of SSU isoforms in plants.
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Affiliation(s)
- Panupon Khumsupan
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Marta A Kozlowska
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Andreas I Andreou
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Naomi Nakayama
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Schenke D, Cai D. Applications of CRISPR/Cas to Improve Crop Disease Resistance: Beyond Inactivation of Susceptibility Factors. iScience 2020; 23:101478. [PMID: 32891884 PMCID: PMC7479627 DOI: 10.1016/j.isci.2020.101478] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Current crop production systems are prone to increasing pathogen pressure. Fundamental understanding of molecular plant-pathogen interactions, the availability of crop and pathogen genomic information, as well as emerging genome editing permits a novel approach for breeding of crop disease resistance. We describe here strategies to identify new targets for resistance breeding with focus on interruption of the compatible plant-pathogen interaction by CRISPR/Cas-mediated genome editing. Basically, crop genome editing can be applied in several ways to achieve this goal. The most common approach focuses on the "simple" knockout by non-homologous end joining repair of plant susceptibility factors required for efficient host colonization. However, genome re-writing via homology-directed repair or base editing can also prevent host manipulation by changing the targets of pathogen-derived effectors or molecules beyond recognition, which also decreases plant susceptibility. We conclude that genome editing by CRISPR/Cas will become increasingly indispensable to generate in relatively short time beneficial resistance traits in crops to meet upcoming challenges.
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Affiliation(s)
- Dirk Schenke
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
| | - Daguang Cai
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
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Fedorova M, Herman RA. Obligatory metabolomic profiling of gene-edited crops is risk disproportionate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1985-1988. [PMID: 32593232 PMCID: PMC7540486 DOI: 10.1111/tpj.14896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/06/2023]
Abstract
It has been argued that the application of metabolomics to gene-edited crops would present value in three areas: (i) the detection of gene-edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk-disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene-edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.
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Affiliation(s)
- Maria Fedorova
- Corteva Agriscience7100 NW 62 AvePO Box 1000JohnstonIA50131USA
| | - Rod A. Herman
- Corteva Agriscience9330 Zionsville RoadIndianapolisIN46268USA
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Subedi U, Jayawardhane KN, Pan X, Ozga J, Chen G, Foroud NA, Singer SD. The Potential of Genome Editing for Improving Seed Oil Content and Fatty Acid Composition in Oilseed Crops. Lipids 2020; 55:495-512. [PMID: 32856292 DOI: 10.1002/lipd.12249] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/16/2022]
Abstract
A continuous rise in demand for vegetable oils, which comprise mainly the storage lipid triacylglycerol, is fueling a surge in research efforts to increase seed oil content and improve fatty acid composition in oilseed crops. Progress in this area has been achieved using both conventional breeding and transgenic approaches to date. However, further advancements using traditional breeding methods will be complicated by the polyploid nature of many oilseed crops and associated time constraints, while public perception and the prohibitive cost of regulatory processes hinders the commercialization of transgenic oilseed crops. As such, genome editing using CRISPR/Cas is emerging as a breakthrough breeding tool that could provide a platform to keep pace with escalating demand while potentially minimizing regulatory burden. In this review, we discuss the technology itself and progress that has been made thus far with respect to its use in oilseed crops to improve seed oil content and quality. Furthermore, we examine a number of genes that may provide ideal targets for genome editing in this context, as well as new CRISPR-related tools that have the potential to be applied to oilseed plants and may allow additional gains to be made in the future.
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Affiliation(s)
- Udaya Subedi
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Kethmi N Jayawardhane
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Xue Pan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Jocelyn Ozga
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada
| | - Nora A Foroud
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, T1J 4B1, AB, Canada
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Veillet F, Kermarrec MP, Chauvin L, Chauvin JE, Nogué F. CRISPR-induced indels and base editing using the Staphylococcus aureus Cas9 in potato. PLoS One 2020; 15:e0235942. [PMID: 32804931 PMCID: PMC7430721 DOI: 10.1371/journal.pone.0235942] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
Genome editing is now widely used in plant science for both basic research and molecular crop breeding. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, through its precision, high efficiency and versatility, allows for editing of many sites in plant genomes. This system has been highly successful to produce knock-out mutants through the introduction of frameshift mutations due to error-prone repair pathways. Nevertheless, recent new CRISPR-based technologies such as base editing and prime editing can generate precise and on demand nucleotide conversion, allowing for fine-tuning of protein function and generating gain-of-function mutants. However, genome editing through CRISPR systems still have some drawbacks and limitations, such as the PAM restriction and the need for more diversity in CRISPR tools to mediate different simultaneous catalytic activities. In this study, we successfully used the CRISPR-Cas9 system from Staphylococcus aureus (SaCas9) for the introduction of frameshift mutations in the tetraploid genome of the cultivated potato (Solanum tuberosum). We also developed a S. aureus-cytosine base editor that mediate nucleotide conversions, allowing for precise modification of specific residues or regulatory elements in potato. Our proof-of-concept in potato expand the plant dicot CRISPR toolbox for biotechnology and precision breeding applications.
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Affiliation(s)
- Florian Veillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
- Germicopa Breeding, Chateauneuf Du Faou, France
- * E-mail:
| | | | - Laura Chauvin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | | | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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Graham N, Patil GB, Bubeck DM, Dobert RC, Glenn KC, Gutsche AT, Kumar S, Lindbo JA, Maas L, May GD, Vega-Sanchez ME, Stupar RM, Morrell PL. Plant Genome Editing and the Relevance of Off-Target Changes. PLANT PHYSIOLOGY 2020; 183:1453-1471. [PMID: 32457089 PMCID: PMC7401131 DOI: 10.1104/pp.19.01194] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 05/07/2020] [Indexed: 05/12/2023]
Abstract
Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
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Affiliation(s)
- Nathaniel Graham
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, Minnesota 55108
- Pairwise, Durham, North Carolina 27709
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | | | | | | | | | | | | | - Luis Maas
- Enza Zaden Research USA, San Juan Bautista, California 95045
| | | | | | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Biswas S, Li R, Hong J, Zhao X, Yuan Z, Zhang D, Shi J. Effective identification of CRISPR/Cas9-induced and naturally occurred mutations in rice using a multiplex ligation-dependent probe amplification-based method. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2323-2334. [PMID: 32405769 DOI: 10.1007/s00122-020-03600-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/01/2020] [Indexed: 05/11/2023]
Abstract
A multiplex ligation-dependent probe amplification (MLPA)-based method was developed and successfully utilized to efficiently detect both CRISPR/Cas9-induced and naturally occurred mutations in rice. The site-specific nuclease-based CRISPR/Cas9 system has emerged as one of the most efficient genome editing tools to modify multiple genomic targets simultaneously in various organisms, including plants for both fundamental and applied researches. Screening for both on-target and off-target mutations in CRISPR/Cas9-generated mutants at the early stages is an indispensable step for functional analysis and subsequent application. Various methods have been developed to detect CRISPR/Cas9-induced mutations in plants. Still, very few have focused on the detection of both on- and off-targets simultaneously, let alone the detection of natural mutations. Here, we report a multiplex capable method that allows to detect CRISPR/Cas9 induced on- and off-target mutations as well as naturally occurred mutation based on a multiplex ligation-dependent probe amplification (MLPA) method. We demonstrated that unlike other methods, the modified target-specific MLPA method can accurately identify any INDELs generated naturally or by the CRISPR/Cas9 system and that it can detect natural variation and zygosity of the CRISPR/Cas9-generated mutants in rice as well. Furthermore, its high sensitivity allowed to define INDELs down to 1 bp and substitutions to a single nucleotide. Therefore, this sensitive, reliable, and cheap method would further accelerate functional analysis and marker-assisted breeding in plants, including rice.
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Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiangxiang Zhao
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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