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Patra S, Chatterjee D, Basak S, Sen S, Mandal A. CRISPR/Cas9 opens new horizon of crop improvement under stress condition. Biochim Biophys Acta Gen Subj 2024; 1868:130685. [PMID: 39079650 DOI: 10.1016/j.bbagen.2024.130685] [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: 11/22/2023] [Revised: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/03/2024]
Abstract
Plants are exposed to a myriad of stresses, stemming from abiotic and biotic sources, significantly threatening agricultural productivity. The low crop yield, coupled with the global burden of population has resulted in the scarcity of quality food, exacerbating socio-economic issues like poverty, hunger, and malnutrition. Conventional breeding methods for the generation of stress-tolerant plants are time-consuming, limit genetic diversity, and are not sustainable for the consistent production of high-yielding crops. In recent years, the use of high-throughput, genome editing (GE) technique has revolutionized the crop-improvement paradigm, ushering greater prospects for agricultural progress. Among these tools, the Clustered regularly interspaced short palindromic repeat (CRISPR), and its associated nuclease protein Cas9, have appeared as a ground-breaking technology, allowing precise knockout (KO), upregulation, and downregulation of target gene expression. Apart from its high efficacy and speed, this programmable nuclease offers exceptional specificity with minimal off-target effects. Here in, we aim to review the latest findings on the application of the CRISPR/Cas9 genome editing tool for generating resilience in plants against environmental stresses.
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Affiliation(s)
- Sanjib Patra
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Debdatta Chatterjee
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Shrabani Basak
- Department of Biological sciences, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata 700091, West Bengal, India
| | - Susmi Sen
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Arunava Mandal
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India.
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Mishra S, Nayak S, Tuteja N, Poosapati S, Swain DM, Sahoo RK. CRISPR/Cas-Mediated Genome Engineering in Plants: Application and Prospectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1884. [PMID: 39065411 PMCID: PMC11279650 DOI: 10.3390/plants13141884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Genetic engineering has become an essential element in developing climate-resilient crops and environmentally sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition-rich, disease-resistant, and stress-tolerant "crops", fruits, and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different aspects of stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign-DNA-free or non-transgenic crops that could be easily regulated for commercialization in most countries.
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Affiliation(s)
- Swetaleena Mishra
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, India;
| | - Subhendu Nayak
- Vidya USA Corporation, Otis Stone Hunter Road, Bunnell, FL 32100, USA;
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India;
| | - Sowmya Poosapati
- Plant Biology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92037, USA
| | - Durga Madhab Swain
- MU Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, India;
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Xuan C, Feng M, Li X, Hou Y, Wei C, Zhang X. Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection. Int J Mol Sci 2024; 25:638. [PMID: 38203810 PMCID: PMC10779513 DOI: 10.3390/ijms25010638] [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: 12/11/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses.
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Affiliation(s)
- Changqing Xuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Mengjiao Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Matinvafa MA, Makani S, Parsasharif N, Zahed MA, Movahed E, Ghiasvand S. CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology. 3 Biotech 2023; 13:383. [PMID: 37920190 PMCID: PMC10618153 DOI: 10.1007/s13205-023-03786-7] [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: 10/29/2022] [Accepted: 09/09/2023] [Indexed: 11/04/2023] Open
Abstract
The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.
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Affiliation(s)
- Mohammad Ali Matinvafa
- Department of Biotechnology & Environment, Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Shadi Makani
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Negin Parsasharif
- Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY USA
| | - Saeedeh Ghiasvand
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Hamedan, Iran
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Yıldırım K, Miladinović D, Sweet J, Akin M, Galović V, Kavas M, Zlatković M, de Andrade E. Genome editing for healthy crops: traits, tools and impacts. FRONTIERS IN PLANT SCIENCE 2023; 14:1231013. [PMID: 37965029 PMCID: PMC10641503 DOI: 10.3389/fpls.2023.1231013] [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: 05/29/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Crop cultivars in commercial use have often been selected because they show high levels of resistance to pathogens. However, widespread cultivation of these crops for many years in the environments favorable to a pathogen requires durable forms of resistance to maintain "healthy crops". Breeding of new varieties tolerant/resistant to biotic stresses by incorporating genetic components related to durable resistance, developing new breeding methods and new active molecules, and improving the Integrated Pest Management strategies have been of great value, but their effectiveness is being challenged by the newly emerging diseases and the rapid change of pathogens due to climatic changes. Genome editing has provided new tools and methods to characterize defense-related genes in crops and improve crop resilience to disease pathogens providing improved food security and future sustainable agricultural systems. In this review, we discuss the principal traits, tools and impacts of utilizing genome editing techniques for achieving of durable resilience and a "healthy plants" concept.
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Affiliation(s)
- Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Ondokuz Mayıs University, Samsun, Türkiye
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jeremy Sweet
- Sweet Environmental Consultants, Cambridge, United Kingdom
| | - Meleksen Akin
- Department of Horticulture, Iğdır University, Iğdır, Türkiye
| | - Vladislava Galović
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Milica Zlatković
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Eugenia de Andrade
- National Institute for Agricultural and Veterinary Research (INIAV), I.P., Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
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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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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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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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Strygina KV, Elatskova AG, Elatskov YA, Tekhanovich GA, Khlestkina EK. Analysis of the Genes That Determine the Dwarf Form of Watermelon Citrullus lanatus (Thunb.) Matsum. & Nakai in the VIR Collection. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Hoffman NE. USDA's revised biotechnology regulation's contribution to increasing agricultural sustainability and responding to climate change. FRONTIERS IN PLANT SCIENCE 2022; 13:1055529. [PMID: 36507369 PMCID: PMC9726801 DOI: 10.3389/fpls.2022.1055529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Biotechnology can provide a valuable tool to meet UN Sustainable Development Goals and U.S. initiatives to find climate solutions and improve agricultural sustainability. The literature contains hundreds of examples of crops that may serve this purpose, yet most remain un-launched due to high regulatory barriers. Recently the USDA revised its biotechnology regulations to make them more risk-proportionate, science-based, and streamlined. Here, we review some of the promising leads that may enable agriculture to contribute to UN sustainability goals. We further describe and discuss how the revised biotechnology regulation would hypothetically apply to these cases.
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Devi R, Chauhan S, Dhillon TS. Genome editing for vegetable crop improvement: Challenges and future prospects. Front Genet 2022; 13:1037091. [PMID: 36482900 PMCID: PMC9723405 DOI: 10.3389/fgene.2022.1037091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/28/2022] [Indexed: 09/10/2024] Open
Abstract
Vegetable crops are known as protective foods due to their potential role in a balanced human diet, especially for vegetarians as they are a rich source of vitamins and minerals along with dietary fibers. Many biotic and abiotic stresses threaten the crop growth, yield and quality of these crops. These crops are annual, biennial and perennial in breeding behavior. Traditional breeding strategies pose many challenges in improving economic crop traits. As in most of the cases the large number of backcrosses and stringent selection pressure is required for the introgression of the useful traits into the germplasm, which is time and labour-intensive process. Plant scientists have improved economic traits like yield, quality, biotic stress resistance, abiotic stress tolerance, and improved nutritional quality of crops more precisely and accurately through the use of the revolutionary breeding method known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9). The high mutation efficiency, less off-target consequences and simplicity of this technique has made it possible to attain novel germplasm resources through gene-directed mutation. It facilitates mutagenic response even in complicated genomes which are difficult to breed using traditional approaches. The revelation of functions of important genes with the advancement of whole-genome sequencing has facilitated the CRISPR-Cas9 editing to mutate the desired target genes. This technology speeds up the creation of new germplasm resources having better agro-economical traits. This review entails a detailed description of CRISPR-Cas9 gene editing technology along with its potential applications in olericulture, challenges faced and future prospects.
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Affiliation(s)
- Ruma Devi
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
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Xu J, Zhang N, Wang K, Xian Q, Dong J, Chen X. Exploring new strategies in diseases resistance of horticultural crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1021350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Horticultural crops are susceptible to various biotic stressors including fungi, oomycetes, bacteria, viruses, and root-knot nematodes. These pathogens limit the growth, development, yield, and quality of horticultural crops, and also limit their adaptability and geographic distribution. The continuous cropping model in horticultural facilities exacerbates soil-borne diseases, and severely restricts yield, quality, and productivity. Recent progress in the understanding of mechanisms that confer tolerance to different diseases through innovative strategies including host-induced gene silencing (HIGS), targeting susceptibility genes, and rootstocks grafting applications are reviewed to systematically explore the resistance mechanisms against horticultural plant diseases. Future work should successfully breed resistant varieties using these strategies combined with molecular biologic methods.
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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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Increasing disease resistance in host plants through genome editing. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Singh J, Sharma D, Brar GS, Sandhu KS, Wani SH, Kashyap R, Kour A, Singh S. CRISPR/Cas tool designs for multiplex genome editing and its applications in developing biotic and abiotic stress-resistant crop plants. Mol Biol Rep 2022; 49:11443-11467. [PMID: 36002653 DOI: 10.1007/s11033-022-07741-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/22/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022]
Abstract
Crop plants are prone to several yield-reducing biotic and abiotic stresses. The crop yield reductions due to these stresses need addressing to maintain an adequate balance between the increasing world population and food production to avoid food scarcities in the future. It is impossible to increase the area under food crops proportionately to meet the rising food demand. In such an adverse scenario overcoming the biotic and abiotic stresses through biotechnological interventions may serve as a boon to help meet the globe's food requirements. Under the current genomic era, the wide availability of genomic resources and genome editing technologies such as Transcription Activator-Like Effector Nucleases (TALENs), Zinc Finger Nucleases (ZFNs), and Clustered-Regularly Interspaced Palindromic Repeats/CRISPR-associated proteins (CRISPR/Cas) has widened the scope of overcoming these stresses for several food crops. These techniques have made gene editing more manageable and accessible with changes at the embryo level by adding or deleting DNA sequences of the target gene(s) from the genome. The CRISPR construct consists of a single guide RNA having complementarity with the nucleotide fragments of the target gene sequence, accompanied by a protospacer adjacent motif. The target sequence in the organism's genome is then cleaved by the Cas9 endonuclease for obtaining a desired trait of interest. The current review describes the components, mechanisms, and types of CRISPR/Cas techniques and how this technology has helped to functionally characterize genes associated with various biotic and abiotic stresses in a target organism. This review also summarizes the application of CRISPR/Cas technology targeting these stresses in crops through knocking down/out of associated genes.
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Affiliation(s)
- Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, 110012, New Delhi, India.,Guru Angad Dev Veterinary and Animal Science University, KVK, Barnala, India
| | - Dimple Sharma
- Department of Food Science and Human Nutrition, Michigan State University, 48824, East Lansing, MI, USA
| | - Gagandeep Singh Brar
- Department of Biological Sciences, North Dakota State University, 58102, Fargo, ND, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, 99163, Pullman, WA, USA
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu, Kashmir, India
| | - Ruchika Kashyap
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, 57007, Brookings, SD, USA
| | - Amardeep Kour
- Regional Research Station, Punjab Agricultural University, 151001, Bathinda, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, 151203, Faridkot, Punjab, India.
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Viviani A, Spada M, Giordani T, Fambrini M, Pugliesi C. Origin of the genome editing systems: application for crop improvement. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Parvathi MS, Antony PD, Kutty MS. Multiple Stressors in Vegetable Production: Insights for Trait-Based Crop Improvement in Cucurbits. FRONTIERS IN PLANT SCIENCE 2022; 13:861637. [PMID: 35592574 PMCID: PMC9111534 DOI: 10.3389/fpls.2022.861637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Vegetable production is a key determinant of contribution from the agricultural sector toward national Gross Domestic Product in a country like India, the second largest producer of fresh vegetables in the world. This calls for a careful scrutiny of the threats to vegetable farming in the event of climate extremes, environmental degradation and incidence of plant pests/diseases. Cucurbits are a vast group of vegetables grown almost throughout the world, which contribute to the daily diet on a global scale. Increasing food supply to cater to the ever-increasing world population, calls for intensive, off-season and year-round cultivation of cucurbits. Current situation predisposes these crops to a multitude of stressors, often simultaneously, under field conditions. This scenario warrants a systematic understanding of the different stress specific traits/mechanisms/pathways and their crosstalk that have been examined in cucurbits and identification of gaps and formulation of perspectives on prospective research directions. The careful dissection of plant responses under specific production environments will help in trait identification for genotype selection, germplasm screens to identify superior donors or for direct genetic manipulation by modern tools for crop improvement. Cucurbits exhibit a wide range of acclimatory responses to both biotic and abiotic stresses, among which a few like morphological characters like waxiness of cuticle; primary and secondary metabolic adjustments; membrane thermostability, osmoregulation and, protein and reactive oxygen species homeostasis and turnover contributing to cellular tolerance, appear to be common and involved in cross talk under combinatorial stress exposures. This is assumed to have profound influence in triggering system level acclimation responses that safeguard growth and metabolism. The possible strategies attempted such as grafting initiatives, molecular breeding, novel genetic manipulation avenues like gene editing and ameliorative stress mitigation approaches, have paved way to unravel the prospects for combined stress tolerance. The advent of next generation sequencing technologies and big data management of the omics output generated have added to the mettle of such emanated concepts and ideas. In this review, we attempt to compile the progress made in deciphering the biotic and abiotic stress responses of cucurbits and their associated traits, both individually and in combination.
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Affiliation(s)
- M. S. Parvathi
- Department of Plant Physiology, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - P. Deepthy Antony
- Centre for Intellectual Property Rights, Technology Management and Trade, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - M. Sangeeta Kutty
- Department of Vegetable Science, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [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: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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20
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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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21
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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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Xuan C, Lan G, Si F, Zeng Z, Wang C, Yadav V, Wei C, Zhang X. Systematic Genome-Wide Study and Expression Analysis of SWEET Gene Family: Sugar Transporter Family Contributes to Biotic and Abiotic Stimuli in Watermelon. Int J Mol Sci 2021; 22:8407. [PMID: 34445115 PMCID: PMC8395094 DOI: 10.3390/ijms22168407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
The SWEET (Sugars Will Eventually be Exported Transporter) proteins are a novel family of sugar transporters that play key roles in sugar efflux, signal transduction, plant growth and development, plant-pathogen interactions, and stress tolerance. In this study, 22 ClaSWEET genes were identified in Citrullus lanatus (Thunb.) through homology searches and classified into four groups by phylogenetic analysis. The genes with similar structures, conserved domains, and motifs were clustered into the same groups. Further analysis of the gene promoter regions uncovered various growth, development, and biotic and abiotic stress responsive cis-regulatory elements. Tissue-specific analysis showed most of the genes were highly expressed in male flowers and the roots of cultivated varieties and wild cultivars. In addition, qRT-PCR results further imply that ClaSWEET proteins might be involved in resistance to Fusarium oxysporum infection. Moreover, a significantly higher expression level of these genes under various abiotic stresses suggests its multifaceted role in mediating plant responses to drought, salt, and low-temperature stress. The genome-wide characterization and phylogenetic analysis of ClaSWEET genes, together with the expression patterns in different tissues and stimuli, lays a solid foundation for future research into their molecular function in watermelon developmental processes and responses to biotic and abiotic stresses.
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Affiliation(s)
- Changqing Xuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Guangpu Lan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Fengfei Si
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Zhilong Zeng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Chunxia Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (C.X.); (G.L.); (F.S.); (Z.Z.); (C.W.); (V.Y.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Mkhize P, Mashilo J, Shimelis H. Progress on Genetic Improvement and Analysis of Bottle Gourd [Lagenaria siceraria (Molina) Standl.] for Agronomic Traits, Nutrient Compositions, and Stress Tolerance: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.683635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bottle gourd [Lagenaria siceraria (Molina) Standl.] is an important multi-purpose cucurbit crop grown for its leaf, fruit, and seed. It is widely cultivated and used for human consumption in sub-Saharan Africa (SSA) providing vital human nutrition and serving as food security crop. There is wide genetic variation among bottle gourd genetic resources in Africa for diverse qualitative and quantitative attributes for effective variety design, product development, and marketing. However, the crop is under- researched and -utilized, and improved varieties are yet to be developed and commercialized in the region. Therefore, the objective of this review is to provide the progress on bottle gourd genetic improvement and genetic analysis targeting agronomic and horticultural attributes, nutritional composition, biotic, and abiotic stress tolerance to guide current and future cultivar development, germplasm access, and conservation in SSA. The first section of the paper presents progress on breeding of bottle gourd for horticultural traits, agronomic performance, nutritional and anti-nutritional composition, and biotic and abiotic stress tolerance. This is followed by important highlights on key genetic resources of cultivated and wild bottle gourd for demand driven breeding. Lastly, the review summaries advances in bottle gourd genomics, genetic engineering and genome editing. Information presented in this paper should aid bottle gourd breeders and agronomists to develop and deploy new generation and promising varieties with farmer- and market -preferred attributes.
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Abstract
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits include a series of backcrosses and selection to introduce beneficial traits into fine germplasm, this process is slow and resource-intensive. The new breeding technique known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9) has the potential to improve many traits rapidly and accurately, such as yield, quality, disease resistance, abiotic stress tolerance, and nutritional aspects in crops. Because of its simple operation and high mutation efficiency, this system has been applied to obtain new germplasm resources via gene-directed mutation. With the availability of whole-genome sequencing data, and information about gene function for important traits, CRISPR-Cas9 editing to precisely mutate key genes can rapidly generate new germplasm resources for the improvement of important agronomic traits. In this review, we explore this technology and its application in fruit and vegetable crops. We address the challenges, existing variants and the associated regulatory framework, and consider future applications.
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25
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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Mishra R, Mohanty JN, Mahanty B, Joshi RK. A single transcript CRISPR/Cas9 mediated mutagenesis of CaERF28 confers anthracnose resistance in chilli pepper (Capsicum annuum L.). PLANTA 2021; 254:5. [PMID: 34132917 DOI: 10.1007/s00425-021-03660-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/10/2021] [Indexed: 05/09/2023]
Abstract
T-DNA-free homozygous mutant lines developed through a single transcript CRISPR/Cas9 system harboring the desired modification in the CaERF28 locus exhibited significantly enhanced resistance to the anthracnose pathogen Colletotrichum truncatum coupled with the improved expression of defense responsive genes. Anthracnose, caused by Colletotrichum species, is a major disease of chilli (Capsicum annuum) accounting for significant pre- and post-harvest yield losses across the tropical and subtropical regions of the world. Management of chilli anthracnose using traditional methods have not met with noticeable success. In the present study, we have demonstrated an enhanced anthracnose resistance through a single transcript unit CRISPR/Cas9 mediated alteration of the susceptibility gene CaERF28 in C. annuum. A construct with a single Pol II promoter-driven expression of Cas9, sgRNA and a hammerhead ribozyme (RZ) was designed to modify the CaERF28 gene in the susceptible chilli genotype Arka Lohit. Fourty-five C-ERF28-induced mutant lines (72.5%) were identified from 62 T0 transgenic plants. Further, simultaneously targeted multiple sites within CaERF28 showed increased mutation (85.7%) efficiency. DNA sequence analysis showed that these plants harboured multiple InDels at the target site. The allelic mutants of C-ERF28 were transferred to the following generations by simple Mendelian inheritance. Segregation in the T1 and T2 generations resulted in the identification of T-DNA free and marker-free C-ERF28 mutant lines. Five homozygous mutants demonstrated enhanced resistance to anthracnose compared to wild type as demonstrated by reduced spore count and fungal growth as well as induced expression of defense-related genes. Our results demonstrated that the STU-CRISPR/Cas9 mediated editing of the CaERF28 gene is a rapid, safe and versatile approach for enhancing anthracnose resistance in chilli pepper and pave way for its utilization in the improvement of other solanaceous crops.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Science, Centurion University of Technology and Management, Bhubaneswar, 752050, India
| | - Jatindra Nath Mohanty
- Centre for Biomedical Informatics, Siksha O Anusandhan University, Bhubaneswar, 751003, India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India.
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Kim YC, Kang Y, Yang EY, Cho MC, Schafleitner R, Lee JH, Jang S. Applications and Major Achievements of Genome Editing in Vegetable Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:688980. [PMID: 34178006 PMCID: PMC8231707 DOI: 10.3389/fpls.2021.688980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 05/04/2023]
Abstract
The emergence of genome-editing technology has allowed manipulation of DNA sequences in genomes to precisely remove or replace specific sequences in organisms resulting in targeted mutations. In plants, genome editing is an attractive method to alter gene functions to generate improved crop varieties. Genome editing is thought to be simple to use and has a lower risk of off-target effects compared to classical mutation breeding. Furthermore, genome-editing technology tools can also be applied directly to crops that contain complex genomes and/or are not easily bred using traditional methods. Currently, highly versatile genome-editing tools for precise and predictable editing of almost any locus in the plant genome make it possible to extend the range of application, including functional genomics research and molecular crop breeding. Vegetables are essential nutrient sources for humans and provide vitamins, minerals, and fiber to diets, thereby contributing to human health. In this review, we provide an overview of the brief history of genome-editing technologies and the components of genome-editing tool boxes, and illustrate basic modes of operation in representative systems. We describe the current and potential practical application of genome editing for the development of improved nutritious vegetables and present several case studies demonstrating the potential of the technology. Finally, we highlight future directions and challenges in applying genome-editing systems to vegetable crops for research and product development.
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Affiliation(s)
- Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Eun-Young Yang
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Myeong-Cheoul Cho
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | | | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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Biswas S, Zhang D, Shi J. CRISPR/Cas systems: opportunities and challenges for crop breeding. PLANT CELL REPORTS 2021; 40:979-998. [PMID: 33977326 DOI: 10.1007/s00299-021-02708-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/28/2021] [Indexed: 05/27/2023]
Abstract
Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.
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Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Li C, Brant E, Budak H, Zhang B. CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 2021; 22:253-284. [PMID: 33835761 PMCID: PMC8042526 DOI: 10.1631/jzus.b2100009] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.
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Affiliation(s)
- Chao Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Eleanor Brant
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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Zhang D, Zhang Z, Unver T, Zhang B. CRISPR/Cas: A powerful tool for gene function study and crop improvement. J Adv Res 2021; 29:207-221. [PMID: 33842017 PMCID: PMC8020163 DOI: 10.1016/j.jare.2020.10.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background It is a long-standing goal of scientists and breeders to precisely control a gene for studying its function as well as improving crop yield, quality, and tolerance to various environmental stresses. The discovery and modification of CRISPR/Cas system, a nature-occurred gene editing tool, opens an era for studying gene function and precision crop breeding. Aim of Review In this review, we first introduce the brief history of CRISPR/Cas discovery followed the mechanism and application of CRISPR/Cas system on gene function study and crop improvement. Currently, CRISPR/Cas genome editing has been becoming a mature cutting-edge biotechnological tool for crop improvement that already used in many different traits in crops, including pathogen resistance, abiotic tolerance, plant development and morphology and even secondary metabolism and fiber development. Finally, we point out the major issues associating with CRISPR/Cas system and the future research directions.Key Scientific Concepts of Review: CRISPR/Cas9 system is a robust and powerful biotechnological tool for targeting an individual DNA and RNA sequence in the genome. It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. Agrobacterium-mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. However, other delivery methods, such as virus-mediated method, have been developed and enhanced the application potentials of CRISPR/Cas9-based crop improvement. PAM requirement offers the CRISPR/Cas9-targted genetic loci and also limits the application of CRISPR/Cas9. Discovering new Cas proteins and modifying current Cas enzymes play an important role in CRISPR/Cas9-based genome editing. Developing a better CRISPR/Cas9 system, including the delivery system and the methods eliminating off-target effects, and finding key/master genes for controlling crop growth and development is two major directions for CRISPR/Cas9-based crop improvement.
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Affiliation(s)
- Dangquan Zhang
- Henan Province Engineering Research Center for Forest Biomass Value-Added Products, College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, No: 1/1/76, 06378, Yenimahalle, Ankara, Turkey
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Bhatta BP, Malla S. Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1360. [PMID: 33066510 PMCID: PMC7602190 DOI: 10.3390/plants9101360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.
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Affiliation(s)
- Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA;
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
| | - Subas Malla
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
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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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