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Khoo YW, Wang Q, Liu S, Zhan B, Xu T, Lv W, Liu G, Li S, Zhang Z. Resistance of the CRISPR-Cas13a Gene-Editing System to Potato Spindle Tuber Viroid Infection in Tomato and Nicotiana benthamiana. Viruses 2024; 16:1401. [PMID: 39339877 PMCID: PMC11437488 DOI: 10.3390/v16091401] [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: 07/05/2024] [Revised: 08/24/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into Nicotiana benthamiana through transgenic methods, using CRISPR RNAs (crRNAs) targeting the conserved regions of both sense and antisense genomes of potato spindle tuber viroid (PSTVd). In tomato plants, the expression of CRISPR-Cas13a and crRNAs substantially reduced PSTVd accumulation and alleviated disease symptoms. In transgenic N. benthamiana plants, the PSTVd levels were lower as compared to wild-type plants. Several effective crRNAs targeting the PSTVd genomic RNA were also identified. These results demonstrate that the CRISPR-Cas13a system can effectively target and combat viroid RNAs, despite their compact structures.
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Affiliation(s)
- Ying Wei Khoo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qingsong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Shangwu Liu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Binhui Zhan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tengfei Xu
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Wenxia Lv
- Inner Mongolia Zhongjia Agricultural Biotechnology Co., Ltd., Ulanqab 011800, China
| | - Guangjing Liu
- Inner Mongolia Zhongjia Agricultural Biotechnology Co., Ltd., Ulanqab 011800, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhixiang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Meng X, Dong T, Li Z, Zhu M. First systematic review of the last 30 years of research on sweetpotato: elucidating the frontiers and hotspots. FRONTIERS IN PLANT SCIENCE 2024; 15:1428975. [PMID: 39036362 PMCID: PMC11258629 DOI: 10.3389/fpls.2024.1428975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024]
Abstract
Sweetpotato is an economically important crop, and it has various advantages over other crops in addressing global food security and climate change. Although substantial articles have been published on the research of various aspects of sweetpotato biology, there are no specific reports to systematically crystallize the research achievements. The current review takes the lead in conducting a keyword-centric spatiotemporal dimensional bibliometric analysis of articles on sweetpotato research using CiteSpace software to comprehensively clarify the development status, research hotspot, and development trend in the past 30 years (1993-2022). Quantitative analysis was carried out on the publishing countries, institutions, disciplines, and scholars to understand the basic status of sweetpotato research; then, visual analysis was conducted on high-frequency keywords, burst keywords, and keyword clustering; the evolution of major research hotspots and the development trend in different periods were summarized. Finally, the three main development stages-preliminary stage (1993-2005), rapid stage (2006-2013), and diversified mature stage (2014-2022)-were reviewed and analyzed in detail. Particularly, the development needs of sweetpotato production in improving breeding efficiency, enhancing stress tolerance, coordinating high yield with high quality and high resistance, and promoting demand were discussed, which will help to comprehensively understand the development dynamics of sweetpotato research from different aspects of biological exploration.
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Affiliation(s)
| | | | | | - Mingku Zhu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
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3
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Pan Z, Li Z, Han Y, Sun J. Genome-Wide Identification and Expression Analysis of the DMP and MTL Genes in Sweetpotato ( Ipomoea batatas L.). Genes (Basel) 2024; 15:354. [PMID: 38540413 PMCID: PMC10970459 DOI: 10.3390/genes15030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
Sweetpotato (Ipomoea batatas L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature of sweetpotato as a hexaploid species (2n = 6x = 90). Double haploid (DH) breeding, based on in vivo haploid induction, provides a new approach for rapid breeding of crops. The success of haploid induction can be achieved by manipulating specific genes. Two of the most critical genes, DMP (DUF679 membrane proteins) and MTL (MATRILINEAL), have been shown to induce haploid production in several species. Here, we identified and characterized DMP and MTL genes in sweetpotato using gene family analysis. In this study, we identified 5 IbDMPs and 25 IbpPLAs. IbDMP5 and IbPLAIIs (IbPLAIIκ, IbPLAIIλ, and IbPLAIIμ) were identified as potential haploid induction (HI) genes in sweetpotato. These results provide valuable information for the identification and potential function of HI genes in sweetpotato and provide ideas for the breeding of DH lines.
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Affiliation(s)
- Zhiyuan Pan
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (Z.P.); (Z.L.)
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (Z.P.); (Z.L.)
| | - Yonghua Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (Z.P.); (Z.L.)
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4
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Ahmed S, Khan MSS, Xue S, Islam F, Ikram AU, Abdullah M, Liu S, Tappiban P, Chen J. A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato. HORTICULTURE RESEARCH 2024; 11:uhae014. [PMID: 38464477 PMCID: PMC10923648 DOI: 10.1093/hr/uhae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/09/2024] [Indexed: 03/12/2024]
Abstract
Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.
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Affiliation(s)
- Sulaiman Ahmed
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | | | - Songlei Xue
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng 224000, China
| | - Faisal Islam
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Aziz Ul Ikram
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minghang, 200240, Shanghai, China
| | - Shan Liu
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Piengtawan Tappiban
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
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Divya K, Thangaraj M, Krishna Radhika N. CRISPR/Cas9: an advanced platform for root and tuber crops improvement. Front Genome Ed 2024; 5:1242510. [PMID: 38312197 PMCID: PMC10836405 DOI: 10.3389/fgeed.2023.1242510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.
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Affiliation(s)
- K Divya
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | | | - N Krishna Radhika
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Kreuze JF, Ramírez DA, Fuentes S, Loayza H, Ninanya J, Rinza J, David M, Gamboa S, De Boeck B, Diaz F, Pérez A, Silva L, Campos H. High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato. Virus Res 2024; 339:199276. [PMID: 38006786 PMCID: PMC10751700 DOI: 10.1016/j.virusres.2023.199276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
Breeders have made important efforts to develop genotypes able to resist virus attacks in sweetpotato, a major crop providing food security and poverty alleviation to smallholder farmers in many regions of Sub-Saharan Africa, Asia and Latin America. However, a lack of accurate objective quantitative methods for this selection target in sweetpotato prevents a consistent and extensive assessment of large breeding populations. In this study, an approach to characterize and classify resistance in sweetpotato was established by assessing total yield loss and virus load after the infection of the three most common viruses (SPFMV, SPCSV, SPLCV). Twelve sweetpotato genotypes with contrasting reactions to virus infection were grown in the field under three different treatments: pre-infected by the three viruses, un-infected and protected from re-infection, and un-infected but exposed to natural infection. Virus loads were assessed using ELISA, (RT-)qPCR, and loop-mediated isothermal amplification (LAMP) methods, and also through multispectral reflectance and canopy temperature collected using an unmanned aerial vehicle. Total yield reduction compared to control and the arithmetic sum of (RT-)qPCR relative expression ratios were used to classify genotypes into four categories: resistant, tolerant, susceptible, and sensitives. Using 14 remote sensing predictors, machine learning algorithms were trained to classify all plots under the said categories. The study found that remotely sensed predictors were effective in discriminating the different virus response categories. The results suggest that using machine learning and remotely sensed data, further complemented by fast and sensitive LAMP assays to confirm results of predicted classifications could be used as a high throughput approach to support virus resistance phenotyping in sweetpotato breeding.
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Affiliation(s)
- Jan F Kreuze
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - David A Ramírez
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Segundo Fuentes
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Hildo Loayza
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru; Programa academico de ingenieria ambiental, Universidad de Huanuco, Jr. Hermilio Valdizan N° 871, Huanuco, Peru.
| | - Johan Ninanya
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Javier Rinza
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Maria David
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Soledad Gamboa
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Bert De Boeck
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Federico Diaz
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Ana Pérez
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Luis Silva
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
| | - Hugo Campos
- International Potato Center (CIP), Headquarters, P.O. Box 1558, Lima 15024, Peru.
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Nie X, Wang D, Pan Y, Hua Y, Lü P, Yang Y. Discovery, classification and application of the CPISPR-Cas13 system. Technol Health Care 2024; 32:525-544. [PMID: 37545273 DOI: 10.3233/thc-230258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins. OBJECTIVE This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance. METHODS Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed. RESULTS The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA. CONCLUSION The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.
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Affiliation(s)
- Xiaojuan Nie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Pan
- School of Experimental Animal Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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8
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Spencer KP, Burger JT, Campa M. CRISPR-based resistance to grapevine virus A. FRONTIERS IN PLANT SCIENCE 2023; 14:1296251. [PMID: 38111883 PMCID: PMC10725905 DOI: 10.3389/fpls.2023.1296251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Introduction Grapevine (Vitis vinifera) is an important fruit crop which contributes significantly to the agricultural sector worldwide. Grapevine viruses are widespread and cause serious diseases which impact the quality and quantity of crop yields. More than 80 viruses plague grapevine, with RNA viruses constituting the largest of these. A recent extension to the clustered regularly interspaced, short palindromic repeat (CRISPR) armory is the Cas13 effector, which exclusively targets single-strand RNA. CRISPR/Cas has been implemented as a defense mechanism in plants, against both DNA and RNA viruses, by being programmed to directly target and cleave the viral genomes. The efficacy of the CRISPR/Cas tool in plants is dependent on efficient delivery of its components into plant cells. Methods To this end, the aim of this study was to use the recent Cas13d variant from Ruminococcus flavefaciens (CasRx) to target the RNA virus, grapevine virus A (GVA). GVA naturally infects grapevine, but can infect the model plant Nicotiana benthamiana, making it a helpful model to study virus infection in grapevine. gRNAs were designed against the coat protein (CP) gene of GVA. N. benthamiana plants expressing CasRx were co-infiltrated with GVA, and with a tobacco rattle virus (TRV)-gRNA expression vector, harbouring a CP gRNA. Results and discussion Results indicated more consistent GVA reductions, specifically gRNA CP-T2, which demonstrated a significant negative correlation with GVA accumulation, as well as multiple gRNA co-infiltrations which similarly showed reduced GVA titre. By establishing a virus-targeting defense system in plants, efficient virus interference mechanisms can be established and applied to major crops, such as grapevine.
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Affiliation(s)
| | | | - Manuela Campa
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Lin J, Yin X, Zeng Y, Hong X, Zhang S, Cui B, Zhu Q, Liang Z, Xue Z, Yang D. Progress and prospect: Biosynthesis of plant natural products based on plant chassis. Biotechnol Adv 2023; 69:108266. [PMID: 37778531 DOI: 10.1016/j.biotechadv.2023.108266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
Plant-derived natural products are a specific class of active substances with numerous applications in the medical, energy, and industrial fields. Many of these substances are in high demand and have become the fundamental materials for various purposes. Recently, the use of synthetic biology to produce plant-derived natural products has become a significant trend. Plant chassis, in particular, offer unique advantages over microbial chassis in terms of cell structure, product affinity, safety, and storage. The development of the plant hairy root tissue culture system has accelerated the commercialization and industrialization of synthetic biology in the production of plant-derived natural products. This paper will present recent progress in the synthesis of various plant natural products using plant chassis, organized by the types of different structures. Additionally, we will summarize the four primary types of plant chassis used for synthesizing natural products from plant sources and review the enabling technologies that have contributed to the development of synthetic biology in recent years. Finally, we will present the role of isolated and combined use of different optimization strategies in breaking the upper limit of natural product production in plant chassis. This review aims to provide practical references for synthetic biologists and highlight the great commercial potential of plant chassis biosynthesis, such as hairy roots.
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Affiliation(s)
- Junjie Lin
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xue Yin
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin 150040, China
| | - Youran Zeng
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xinyu Hong
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Shuncang Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Qinlong Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zongsuo Liang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin 150040, China..
| | - Dongfeng Yang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China; Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, China.
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Yang Y, Chen Y, Bo Y, Liu Q, Zhai H. Research Progress in the Mechanisms of Resistance to Biotic Stress in Sweet Potato. Genes (Basel) 2023; 14:2106. [PMID: 38003049 PMCID: PMC10671456 DOI: 10.3390/genes14112106] [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: 10/12/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important food, feed, industrial raw materials, and new energy crops, and is widely cultivated around the world. China is the largest sweet potato producer in the world, and the sweet potato industry plays an important role in China's agriculture. During the growth of sweet potato, it is often affected by biotic stresses, such as fungi, nematodes, insects, viruses, and bacteria. These stressors are widespread worldwide and have severely restricted the production of sweet potato. In recent years, with the rapid development and maturity of biotechnology, an increasing number of stress-related genes have been introduced into sweet potato, which improves its quality and resistance of sweet potato. This paper summarizes the discovery of biological stress-related genes in sweet potato and the related mechanisms of stress resistance from the perspectives of genomics analysis, transcriptomics analysis, genetic engineering, and physiological and biochemical indicators. The mechanisms of stress resistance provide a reference for analyzing the molecular breeding of disease resistance mechanisms and biotic stress resistance in sweet potato.
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Affiliation(s)
| | | | | | | | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (Y.Y.); (Y.C.); (Y.B.); (Q.L.)
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11
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Shahriari Z, Su X, Zheng K, Zhang Z. Advances and Prospects of Virus-Resistant Breeding in Tomatoes. Int J Mol Sci 2023; 24:15448. [PMID: 37895127 PMCID: PMC10607384 DOI: 10.3390/ijms242015448] [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: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.
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Affiliation(s)
- Zolfaghar Shahriari
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
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12
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Sardar A. Genetic amelioration of fruit and vegetable crops to increase biotic and abiotic stress resistance through CRISPR Genome Editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1260102. [PMID: 37841604 PMCID: PMC10570431 DOI: 10.3389/fpls.2023.1260102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Environmental changes and increasing population are major concerns for crop production and food security as a whole. To address this, researchers had focussed on the improvement of cereals and pulses and have made considerable progress till the beginning of this decade. However, cereals and pulses together, without vegetables and fruits, are inadequate to meet the dietary and nutritional demands of human life. Production of good quality vegetables and fruits is highly challenging owing to their perishable nature and short shelf life as well as abiotic and biotic stresses encountered during pre- and post-harvest. Genetic engineering approaches to produce good quality, to increase shelf life and stress-resistance, and to change the time of flowering and fruit ripening by introducing foreign genes to produce genetically modified crops were quite successful. However, several biosafety concerns, such as the risk of transgene-outcrossing, limited their production, marketing, and consumption. Modern genome editing techniques, like the CRISPR/Cas9 system, provide a perfect solution in this scenario, as it can produce transgene-free genetically edited plants. Hence, these genetically edited plants can easily satisfy the biosafety norms for crop production and consumption. This review highlights the potential of the CRISPR/Cas9 system for the successful generation of abiotic and biotic stress resistance and thereby improving the quality, yield, and overall productivity of vegetables and fruits.
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Affiliation(s)
- Atish Sardar
- Department of Botany, Jogesh Chandra Chaudhuri College, West Bengal, Kolkata, India
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Kasi Viswanath K, Hamid A, Ateka E, Pappu HR. CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management. PHYTOPATHOLOGY 2023; 113:1661-1676. [PMID: 37486077 DOI: 10.1094/phyto-01-23-0002-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.
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Affiliation(s)
| | - Aflaq Hamid
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
| | - Elijah Ateka
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
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Zhan X, Liu W, Nie B, Zhang F, Zhang J. Cas13d-mediated multiplex RNA targeting confers a broad-spectrum resistance against RNA viruses in potato. Commun Biol 2023; 6:855. [PMID: 37591976 PMCID: PMC10435558 DOI: 10.1038/s42003-023-05205-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
CRISPR-Cas systems endow the bacterial and archaeal species with adaptive immune mechanisms to fend off invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13d has been harnessed to confer the protection against RNA viruses in diverse eukaryotic species. However a vast number of different viruses can potentially infect the same host plant resulting in mixed infection, thus necessitating the generation of crops with broad-spectrum resistance to multiple viruses. Here we report the repurposing of CRISPR/Cas13d coupled with an endogenous tRNA-processing system (polycistronic tRNA-gRNA, PTG) to target the multiple potato RNA viruses. Expression of Cas13d and four different gRNAs were observed in transgenic potato lines expressing the Cas13d/PTG construct. We show that the Cas13d/PTG transgenic plants exhibit resistance to either PVY, PVS, PVX or PLRV alone or two/three viruses simultaneously by reducing viral accumulation in plant cells. In sum, our findings provide an efficient strategy for engineering crops that can simultaneously resist infection by multiple RNA viruses.
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Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenting Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Bihua Nie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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Phan HTL, Kim K, Lee H, Seong JK. Progress in and Prospects of Genome Editing Tools for Human Disease Model Development and Therapeutic Applications. Genes (Basel) 2023; 14:483. [PMID: 36833410 PMCID: PMC9957140 DOI: 10.3390/genes14020483] [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: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Programmable nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas, are widely accepted because of their diversity and enormous potential for targeted genomic modifications in eukaryotes and other animals. Moreover, rapid advances in genome editing tools have accelerated the ability to produce various genetically modified animal models for studying human diseases. Given the advances in gene editing tools, these animal models are gradually evolving toward mimicking human diseases through the introduction of human pathogenic mutations in their genome rather than the conventional gene knockout. In the present review, we summarize the current progress in and discuss the prospects for developing mouse models of human diseases and their therapeutic applications based on advances in the study of programmable nucleases.
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Affiliation(s)
- Hong Thi Lam Phan
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, Republic of Korea
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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Wang Y, Zafar N, Ali Q, Manghwar H, Wang G, Yu L, Ding X, Ding F, Hong N, Wang G, Jin S. CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:3928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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Affiliation(s)
- Yaxin Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Naeem Zafar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qurban Ali
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hakim Manghwar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Ding
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Tuncel A, Qi Y. CRISPR/Cas mediated genome editing in potato: Past achievements and future directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111474. [PMID: 36174801 DOI: 10.1016/j.plantsci.2022.111474] [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: 06/20/2022] [Revised: 08/29/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.
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Affiliation(s)
- Aytug Tuncel
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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20
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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Samarfard S, Ghorbani A, Karbanowicz TP, Lim ZX, Saedi M, Fariborzi N, McTaggart AR, Izadpanah K. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. J Biotechnol 2022; 359:82-94. [PMID: 36174794 DOI: 10.1016/j.jbiotec.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.
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Affiliation(s)
- Samira Samarfard
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, the Islamic Republic of Iran.
| | | | - Zhi Xian Lim
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mahshid Saedi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, the Islamic Republic of Iran
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, the Islamic Republic of Iran
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Keramatollah Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, the Islamic Republic of Iran
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22
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Chen S, Mo Y, Zhang Y, Zhu H, Ling Y. Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing. PLANTA 2022; 256:72. [PMID: 36083517 DOI: 10.1007/s00425-022-03965-5] [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: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.
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Affiliation(s)
- Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Hongbao Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
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23
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Applications of CRISPR/Cas13-Based RNA Editing in Plants. Cells 2022; 11:cells11172665. [PMID: 36078073 PMCID: PMC9454418 DOI: 10.3390/cells11172665] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is widely used as a genome-editing tool in various organisms, including plants, to elucidate the fundamental understanding of gene function, disease diagnostics, and crop improvement. Among the CRISPR/Cas systems, Cas9 is one of the widely used nucleases for DNA modifications, but manipulation of RNA at the post-transcriptional level is limited. The recently identified type VI CRISPR/Cas systems provide a platform for precise RNA manipulation without permanent changes to the genome. Several studies reported efficient application of Cas13 in RNA studies, such as viral interference, RNA knockdown, and RNA detection in various organisms. Cas13 was also used to produce virus resistance in plants, as most plant viruses are RNA viruses. However, the application of CRISPR/Cas13 to studies of plant RNA biology is still in its infancy. This review discusses the current and prospective applications of CRISPR/Cas13-based RNA editing technologies in plants.
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Gentzel IN, Ohlson EW, Redinbaugh MG, Wang GL. VIGE: virus-induced genome editing for improving abiotic and biotic stress traits in plants. STRESS BIOLOGY 2022; 2:2. [PMID: 37676518 PMCID: PMC10441944 DOI: 10.1007/s44154-021-00026-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/12/2021] [Indexed: 09/08/2023]
Abstract
Agricultural production is hampered by disease, pests, and environmental stresses. To minimize yield loss, it is important to develop crop cultivars with resistance or tolerance to their respective biotic and abiotic constraints. Transformation techniques are not optimized for many species and desirable cultivars may not be amenable to genetic transformation, necessitating inferior cultivar usage and time-consuming introgression through backcrossing to the preferred variety. Overcoming these limitations will greatly facilitate the development of disease, insect, and abiotic stress tolerant crops. One such avenue for rapid crop improvement is the development of viral systems to deliver CRISPR/Cas-based genome editing technology to plants to generate targeted beneficial mutations. Viral delivery of genomic editing constructs can theoretically be applied to span the entire host range of the virus utilized, circumventing the challenges associated with traditional transformation and breeding techniques. Here we explore the types of viruses that have been optimized for CRISPR/Cas9 delivery, the phenotypic outcomes achieved in recent studies, and discuss the future potential of this rapidly advancing technology.
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Affiliation(s)
- Irene N Gentzel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Erik W Ohlson
- USDA, Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | | | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
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