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Mat Jalaluddin NS, Ahmad Fuaad AAH, Othman RY. Regulatory landscape and public perception for gene-edited bananas in the Southeast Asian region. Transgenic Res 2024; 33:89-97. [PMID: 38600337 DOI: 10.1007/s11248-024-00379-9] [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: 01/29/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Banana is a premier fruit crop in many parts of the world especially Southeast Asia. The demand for banana has contributed to significant national income to primary banana producers in the SEA region such as the Philippines, Indonesia, Thailand, Vietnam, and Malaysia. However, the widely traded banana industry is plagued by numerous threats including pests and diseases, post-harvest issues and extreme climate vulnerability. To address these challenges, new breeding techniques such as gene editing have been explored for breeding programs to develop improved banana varieties. The first gene-edited non-browning banana has been deregulated in the Philippines recently, and more regulatory applications are expected to submit for approvals soon. Hence, it is timely to review the policy options for gene editing that have been adopted and discussed in the Southeast Asian countries and highlight the implications of differing regulatory approaches to gene editing for trading activities. Positive stakeholders' perceptions and public acceptance are key factors in allowing the benefits of gene editing and thus appropriate outreach strategies are important to gain acceptance and avoid the "GMO stigma" that may be associated with gene-edited products.
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Affiliation(s)
- Nurzatil Sharleeza Mat Jalaluddin
- Department of Science and Technology Studies, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | | | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Institute of Advance Studies, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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2
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Sojka J, Šamajová O, Šamaj J. Gene-edited protein kinases and phosphatases in molecular plant breeding. TRENDS IN PLANT SCIENCE 2024; 29:694-710. [PMID: 38151445 DOI: 10.1016/j.tplants.2023.11.019] [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: 07/13/2023] [Revised: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Protein phosphorylation, the most common and essential post-translational modification, belongs to crucial regulatory mechanisms in plants, affecting their metabolism, intracellular transport, cytoarchitecture, cell division, growth, development, and interactions with the environment. Protein kinases and phosphatases, two important families of enzymes optimally regulating phosphorylation, have now become important targets for gene editing in crops. We review progress on gene-edited protein kinases and phosphatases in crops using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). We also provide guidance for computational prediction of alterations and/or changes in function, activity, and binding of protein kinases and phosphatases as consequences of CRISPR/Cas9-based gene editing with its possible application in modern crop molecular breeding towards sustainable agriculture.
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Affiliation(s)
- Jiří Sojka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
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3
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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [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: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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4
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Ho T, Broome JC, Buhler JP, O'Donovan W, Tian T, Diaz-Lara A, Martin RR, Tzanetakis IE. Integration of Rubus yellow net virus in the raspberry genome: A story centuries in the making. Virology 2024; 591:109991. [PMID: 38242059 DOI: 10.1016/j.virol.2024.109991] [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: 10/29/2023] [Revised: 12/16/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs.
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Affiliation(s)
- Thien Ho
- Driscoll's Inc., Watsonville, CA, 95076, USA.
| | | | | | | | - Tongyan Tian
- California Department of Food and Agriculture, Sacramento, CA 95832, USA
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Robert R Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA; USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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5
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Campa M, Miranda S, Licciardello C, Lashbrooke JG, Dalla Costa L, Guan Q, Spök A, Malnoy M. Application of new breeding techniques in fruit trees. PLANT PHYSIOLOGY 2024; 194:1304-1322. [PMID: 37394947 DOI: 10.1093/plphys/kiad374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
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Affiliation(s)
- Manuela Campa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Simón Miranda
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | | | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Mickael Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
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6
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Rengasamy B, Manna M, Thajuddin NB, Sathiyabama M, Sinha AK. Breeding rice for yield improvement through CRISPR/Cas9 genome editing method: current technologies and examples. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:185-198. [PMID: 38623165 PMCID: PMC11016042 DOI: 10.1007/s12298-024-01423-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/23/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
The impending climate change is threatening the rice productivity of the Asian subcontinent as instances of crop failures due to adverse abiotic and biotic stress factors are becoming common occurrences. CRISPR-Cas9 mediated genome editing offers a potential solution for improving rice yield as well as its stress adaptation. This technology allows modification of plant's genetic elements and is not dependent on foreign DNA/gene insertion for incorporating a particular trait. In this review, we have discussed various CRISPR-Cas9 mediated genome editing tools for gene knockout, gene knock-in, simultaneously disrupting multiple genes by multiplexing, base editing and prime editing the genes. The review here also presents how these genome editing technologies have been employed to improve rice productivity by directly targeting the yield related genes or by indirectly manipulating various abiotic and biotic stress responsive genes. Lately, many countries treat genome-edited crops as non-GMOs because of the absence of foreign DNA in the final product. Thus, genome edited rice plants with improved yield attributes and stress resilience are expected to be accepted by the public and solve food crisis of a major portion of the globe. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01423-y.
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Affiliation(s)
- Balakrishnan Rengasamy
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Mrinalini Manna
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Nargis Begum Thajuddin
- P. G. and Research Department of Biotechnology, Jamal Mohamed College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
| | | | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
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7
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [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: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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8
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Saini H, Thakur R, Gill R, Tyagi K, Goswami M. CRISPR/Cas9-gene editing approaches in plant breeding. GM CROPS & FOOD 2023; 14:1-17. [PMID: 37725519 PMCID: PMC10512805 DOI: 10.1080/21645698.2023.2256930] [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: 03/06/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
CRISPR/Cas9 gene editing system is recently developed robust genome editing technology for accelerating plant breeding. Various modifications of this editing system have been established for adaptability in plant varieties as well as for its improved efficiency and portability. This review provides an in-depth look at the various strategies for synthesizing gRNAs for efficient delivery in plant cells, including chemical synthesis and in vitro transcription. It also covers traditional analytical tools and emerging developments in detection methods to analyze CRISPR/Cas9 mediated mutation in plant breeding. Additionally, the review outlines the various analytical tools which are used to detect and analyze CRISPR/Cas9 mediated mutations, such as next-generation sequencing, restriction enzyme analysis, and southern blotting. Finally, the review discusses emerging detection methods, including digital PCR and qPCR. Hence, CRISPR/Cas9 has great potential for transforming agriculture and opening avenues for new advancements in the system for gene editing in plants.
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Affiliation(s)
- Himanshu Saini
- School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
- School of Agriculture, Forestry & Fisheries, Himgiri Zee University, Dehradun, Uttarakhand, India
| | - Rajneesh Thakur
- Department of Plant Pathology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, India
| | - Rubina Gill
- Department of Agronomy, School of Agriculture, Lovely professional university, Phagwara, Punjab, India
| | - Kalpana Tyagi
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, India
| | - Manika Goswami
- Department of Fruit Science, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, India
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9
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Rao X, Chen H, Lu Y, Liu R, Li H. Distribution and Location of BEVs in Different Genotypes of Bananas Reveal the Coevolution of BSVs and Bananas. Int J Mol Sci 2023; 24:17064. [PMID: 38069393 PMCID: PMC10707546 DOI: 10.3390/ijms242317064] [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: 10/21/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Members of the family Caulimoviridae contain abundant endogenous pararetroviral sequences (EPRVs) integrated into the host genome. Banana streak virus (BSV), a member of the genus Badnavirus in this family, has two distinct badnaviral integrated sequences, endogenous BSV (eBSV) and banana endogenous badnavirus sequences (BEVs). BEVs are distributed widely across the genomes of different genotypes of bananas. To clarify the distribution and location of BEVs in different genotypes of bananas and their coevolutionary relationship with bananas and BSVs, BEVs and BSVs were identified in 102 collected banana samples, and a total of 327 BEVs were obtained and categorized into 26 BEVs species with different detection rates. However, the majority of BEVs were found in Clade II, and a few were clustered in Clade I. Additionally, BEVs and BSVs shared five common conserved motifs. However, BEVs had two unique amino acids, methionine and lysine, which differed from BSVs. BEVs were distributed unequally on most of chromosomes and formed hotspots. Interestingly, a colinear relationship of BEVs was found between AA and BB, as well as AA and SS genotypes of bananas. Notably, the chromosome integration time of different BEVs varied. Based on our findings, we propose that the coevolution of bananas and BSVs is driven by BSV Driving Force (BDF), a complex interaction between BSVs, eBSVs, and BEVs. This study provides the first clarification of the relationship between BEVs and the coevolution of BSVs and bananas in China.
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Affiliation(s)
| | | | | | | | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (X.R.); (H.C.); (Y.L.); (R.L.)
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10
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Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
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Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
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11
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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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12
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Jacobson S, Bondarchuk N, Nguyen TA, Canada A, McCord L, Artlip TS, Welser P, Klocko AL. Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple. PLANTS (BASEL, SWITZERLAND) 2023; 12:3693. [PMID: 37960050 PMCID: PMC10649517 DOI: 10.3390/plants12213693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.
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Affiliation(s)
- Seth Jacobson
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Natalie Bondarchuk
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Thy Anh Nguyen
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Allison Canada
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Logan McCord
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Timothy S. Artlip
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Philipp Welser
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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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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14
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Jalilian A, Bagheri A, Chalvon V, Meusnier I, Kroj T, Kakhki AM. The RLCK subfamily VII-4 controls pattern-triggered immunity and basal resistance to bacterial and fungal pathogens in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1345-1356. [PMID: 37248636 DOI: 10.1111/tpj.16323] [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: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Receptor-like cytoplasmic kinases (RLCKs) mediate the intracellular signaling downstream of pattern-recognition receptors (PRRs). Several RLCKs from subfamily VII of rice (Oryza sativa) have important roles in plant immunity, but the role of RLCK VII-4 in pattern-triggered immune (PTI) signaling and resistance to pathogens has not yet been investigated. Here, we generated by multiplex clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing rice sextuple mutant lines where the entire RLCK VII-4 subfamily is inactivated and then analyzed the resulting lines for their response to chitin and flg22 and for their immunity to Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae. Analysis of the rlckvii-4 mutants revealed that they have an impaired reactive oxygen system burst and reduced defense gene expression in response to flg22 and chitin. This indicates that members of the rice RLCK VII-4 subfamily are required for immune signaling downstream of multiple PRRs. Furthermore, we found that the rice RLCK VII-4 subfamily is important for chitin-induced callose deposition and mitogen-activated protein kinase activation and that it is crucial for basal resistance against Xoo and M. oryzae pathogens. This establishes that the RLCK VII-4 subfamily has critical functions in the regulation of multiple PTI pathways in rice and opens the way for deciphering the precise role of its members in the control of rice PTI.
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Affiliation(s)
- Ahmad Jalilian
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Isabelle Meusnier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institute Agro, IRD, Montpellier, France
| | - Amin Mirshamsi Kakhki
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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15
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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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16
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Erdoğan İ, Cevher-Keskin B, Bilir Ö, Hong Y, Tör M. Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance. BIOLOGY 2023; 12:1037. [PMID: 37508466 PMCID: PMC10376527 DOI: 10.3390/biology12071037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.
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Affiliation(s)
- İbrahim Erdoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Kirsehir Ahi Evran University, Kırşehir 40100, Türkiye
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - Birsen Cevher-Keskin
- Genetic Engineering and Biotechnology Institute, TÜBİTAK Marmara Research Center, Kocaeli 41470, Türkiye
| | - Özlem Bilir
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
- Trakya Agricultural Research Institute, Atatürk Bulvarı 167/A, Edirne 22100, Türkiye
| | - Yiguo Hong
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
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Adero M, Tripathi JN, Tripathi L. Advances in Somatic Embryogenesis of Banana. Int J Mol Sci 2023; 24:10999. [PMID: 37446177 DOI: 10.3390/ijms241310999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The cultivation of bananas and plantains (Musa spp.) holds significant global economic importance, but faces numerous challenges, which may include diverse abiotic and biotic factors such as drought and various diseases caused by fungi, viruses, and bacteria. The genetic and asexual nature of cultivated banana cultivars makes them unattractive for improvement via traditional breeding. To overcome these constraints, modern biotechnological approaches like genetic modification and genome editing have become essential for banana improvement. However, these techniques rely on somatic embryogenesis, which has only been successfully achieved in a limited number of banana cultivars. Therefore, developing new strategies for improving somatic embryogenesis in banana is crucial. This review article focuses on advancements in banana somatic embryogenesis, highlighting the progress, the various stages of regeneration, cryopreservation techniques, and the molecular mechanisms underlying the process. Furthermore, this article discusses the factors that could influence somatic embryogenesis and explores the prospects for improving the process, especially in recalcitrant banana cultivars. By addressing these challenges and exploring potential solutions, researchers aim to unlock the full potential of somatic embryogenesis as a tool for banana improvement, ultimately benefiting the global banana industry.
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Affiliation(s)
- Mark Adero
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya
| | | | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya
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18
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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [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: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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Jogam P, Sandhya D, Alok A, Peddaboina V, Singh SP, Abbagani S, Zhang B, Allini VR. Editing of TOM1 gene in tobacco using CRISPR/Cas9 confers resistance to Tobacco mosaic virus. Mol Biol Rep 2023; 50:5165-5176. [PMID: 37119416 DOI: 10.1007/s11033-023-08440-2] [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: 10/13/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND Genome editing technology has become one of the excellent tools for precise plant breeding to develop novel plant germplasm. The Tobacco mosaic virus (TMV) is the most prominent pathogen that infects several Solanaceae plants, such as tobacco, tomato, and capsicum, which requires critical host factors for infection and replication of its genomic RNA in the host. The Tobamovirus multiplication (TOM) genes, such as TOM1, TOM2A, TOM2B, and TOM3, are involved in the multiplication of Tobamoviruses. TOM1 is a transmembrane protein necessary for efficient TMV multiplication in several plant species. The TOM genes are crucial recessive resistance genes that act against the tobamoviruses in various plant species. METHODS AND RESULTS The single guided RNA (sgRNA) was designed to target the first exon of the NtTOM1 gene and cloned into the pHSE401 vector. The pHSE401-NtTOM1 vector was introduced into Agrobacterium tumefaciens strain LBA4404 and then transformed into tobacco plants. The analysis on T0 transgenic plants showed the presence of the hptII and Cas9 transgenes. The sequence analysis of the NtTOM1 from T0 plants showed the indels. Genotypic evaluation of the NtTOM1 mutant lines displayed the stable inheritance of the mutations in the subsequent generations of tobacco plants. The NtTOM1 mutant lines successfully conferred resistance to TMV. CONCLUSIONS CRISPR/Cas genome editing is a reliable tool for investigating gene function and precision breeding across different plant species, especially the species in the Solanaceae family.
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Affiliation(s)
- Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | | | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, 140306, Punjab, India
| | - Sadanandam Abbagani
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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20
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Hemalatha P, Abda EM, Shah S, Venkatesa Prabhu S, Jayakumar M, Karmegam N, Kim W, Govarthanan M. Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117382. [PMID: 36753844 DOI: 10.1016/j.jenvman.2023.117382] [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: 12/09/2022] [Revised: 01/14/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.
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Affiliation(s)
- Palanivel Hemalatha
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Ebrahim M Abda
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Shipra Shah
- Department of Forestry, College of Agriculture, Fisheries and Forestry, Fiji National University, Kings Road, Koronivia, P. O. Box 1544, Nausori, Republic of Fiji
| | - S Venkatesa Prabhu
- Department of Chemical Engineering, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - M Jayakumar
- Department of Chemical Engineering, Haramaya Institute of Technology, Haramaya University, P.O. Box 138, Dire Dawa, Ethiopia.
| | - N Karmegam
- PG and Research Department of Botany, Government Arts College (Autonomous), Salem, 636 007, Tamil Nadu, India
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - M Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, 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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22
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Boubakri H. Recent progress in CRISPR/Cas9-based genome editing for enhancing plant disease resistance. Gene 2023; 866:147334. [PMID: 36871676 DOI: 10.1016/j.gene.2023.147334] [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: 07/20/2022] [Revised: 12/22/2022] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Nowadays, agricultural production is strongly affected by both climate change and pathogen attacks which seriously threaten global food security. For a long time, researchers have been waiting for a tool allowing DNA/RNA manipulation to tailor genes and their expression. Some earlier genetic manipulation methods such as meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) allowed site directed modification but their successful rate was limited due to lack of flexibility when targeting a 'site-specific nucleic acid'. The discovery of clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has revolutionized genome editing domain in different living organisms during the past 9 years. Based on RNA-guided DNA/RNA recognition, CRISPR/Cas9 optimizations have offered an unrecorded scientific opportunity to engineer plants resistant to diverse pathogens. In this report, we describe the main characteristics of the primary reported-genome editing tools ((MNs, ZFNs, TALENs) and evaluate the different CRISPR/Cas9 methods and achievements in developing crop plants resistant to viruses, fungi and bacteria.
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Affiliation(s)
- Hatem Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia.
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Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [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: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
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Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
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24
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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Baer M, Taramino G, Multani D, Sakai H, Jiao S, Fengler K, Hochholdinger F. Maize lateral rootless 1 encodes a homolog of the DCAF protein subunit of the CUL4-based E3 ubiquitin ligase complex. THE NEW PHYTOLOGIST 2023; 237:1204-1214. [PMID: 36345913 DOI: 10.1111/nph.18599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
In maize (Zea mays L.), lateral roots are formed in the differentiation zone of all root types in a multi-step process. The maize mutant lateral rootless 1 (lrt1) is defective in lateral root formation in primary and seminal roots but not in shoot-borne roots. We cloned the lrt1 gene by mapping in combination with BSA-seq and subsequent validation via CRISPR/Cas9. The lrt1 gene encodes a 209 kDa homolog of the DDB1-CUL4-ASSOCIATED FACTOR (DCAF) subunit of the CUL4-based E3 ubiquitin ligase (CRL4) complex localized in the nucleus. DDB1-CUL4-ASSOCIATED FACTOR proteins are encoded by an evolutionary old gene family already present in nonseed plants. They are adaptors that bind substrate proteins and promote their ubiquitylation, thus typically marking them for subsequent degradation in the 26S proteasome. Gene expression studies demonstrated that lrt1 transcripts are expressed preferentially in the meristematic zone of all root types of maize. Downregulation of the rum1 gene in lrt1 mutants suggests that lrt1 acts upstream of the lateral root regulator rum1. Our results demonstrate that DCAF proteins play a key role in root-type-specific lateral root formation in maize. Together with its role in nitrogen acquisition in nitrogen-poor soil, lrt1 could be a promising target for maize improvement.
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Affiliation(s)
- Marcel Baer
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | | | | | | | | | | | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
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Biotechnological interventions in reducing losses of tropical fruits and vegetables. Curr Opin Biotechnol 2023; 79:102850. [PMID: 36481342 DOI: 10.1016/j.copbio.2022.102850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022]
Abstract
Tropical fruits and vegetables are predominantly cultivated in warm climate zones, resulting in cultivar diversity in terms of structure, features, and physiology. These constitute a variety of bioactive ingredients such as vitamins, minerals, phenolic acids, anthocyanins, flavonoids, fatty acids, fiber, and their distinctive appearances attract customers across the world. The global production of fruit and vegetables has been attained a tremendous increase for the last few decades. However, huge losses at pre- and postharvest levels are major constraints in their judicious use. Traditional breeding strategies were used to minimize these losses, but their functionality is limited due to their time and labor intensiveness. Recent biotechnological, computational, and multiomics approaches not only address the losses concern but also aid in boosting crop productivity and nutritional values. This article emphasizes molecular tools that have been used to reduce losses of tropical fruits and vegetables at pre- and postharvest levels.
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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Kumar M, Prusty MR, Pandey MK, Singh PK, Bohra A, Guo B, Varshney RK. Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1157678. [PMID: 37143874 PMCID: PMC10153630 DOI: 10.3389/fpls.2023.1157678] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reducing global agricultural production. Traditional breeding approaches and transgenic technology have been widely used to mitigate the risks of these environmental stresses. The discovery of engineered nucleases as genetic scissors to carry out precise manipulation in crop stress-responsive genes and associated molecular network has paved the way for sustainable management of abiotic stress conditions. In this context, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas)-based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the latest findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas-mediated gene-editing system towards enhanced tolerance to a multitude of stresses including drought, salinity, cold, heat, and heavy metals. We provide mechanistic insights on the CRISPR/Cas9-based genome editing technology. We also discuss applications of evolving genome editing techniques such as prime editing and base editing, mutant library production, transgene free and multiplexing to rapidly deliver modern crop cultivars adapted to abiotic stress conditions.
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Affiliation(s)
- Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
| | - Manas Ranjan Prusty
- Institute for Cereal Crop Improvement, Plant Science, Tel Aviv University, Tel Aviv, Israel
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College, Aizawl, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Baozhu Guo
- Crop Genetics and Breeding Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA, United States
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
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Sharma P, Pandey A, Malviya R, Dey S, Karmakar S, Gayen D. Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals. Front Genome Ed 2023; 5:1094965. [PMID: 36911238 PMCID: PMC9998953 DOI: 10.3389/fgeed.2023.1094965] [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: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Agricultural production relies on horticultural crops, including vegetables, fruits, and ornamental plants, which sustain human life. With an alarming increase in human population and the consequential need for more food, it has become necessary for increased production to maintain food security. Conventional breeding has subsidized the development of improved verities but to enhance crop production, new breeding techniques need to be acquired. CRISPR-Cas9 system is a unique and powerful genome manipulation tool that can change the DNA in a precise way. Based on the bacterial adaptive immune system, this technique uses an endonuclease that creates double-stranded breaks (DSBs) at the target loci under the guidance of a single guide RNA. These DSBs can be repaired by a cellular repair mechanism that installs small insertion and deletion (indels) at the cut sites. When equated to alternate editing tools like ZFN, TALENs, and meganucleases, CRISPR- The cas-based editing tool has quickly gained fast-forward for its simplicity, ease to use, and low off-target effect. In numerous horticultural and industrial crops, the CRISPR technology has been successfully used to enhance stress tolerance, self-life, nutritional improvements, flavor, and metabolites. The CRISPR-based tool is the most appropriate one with the prospective goal of generating non-transgenic yields and avoiding the regulatory hurdles to release the modified crops into the market. Although several challenges for editing horticultural, industrial, and ornamental crops remain, this new novel nuclease, with its crop-specific application, makes it a dynamic tool for crop improvement.
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Affiliation(s)
- Punam Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | | | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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Tripathi S, Khatri P, Fatima Z, Pandey RP, Hameed S. A Landscape of CRISPR/Cas Technique for Emerging Viral Disease Diagnostics and Therapeutics: Progress and Prospects. Pathogens 2022; 12:pathogens12010056. [PMID: 36678404 PMCID: PMC9863163 DOI: 10.3390/pathogens12010056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Viral diseases have emerged as a serious threat to humanity and as a leading cause of morbidity worldwide. Many viral diagnostic methods and antiviral therapies have been developed over time, but we are still a long way from treating certain infections caused by viruses. Acquired immunodeficiency syndrome (AIDS) is one of the challenges where current medical science advancements fall short. As a result, new diagnostic and treatment options are desperately needed. The CRISPR/Cas9 system has recently been proposed as a potential therapeutic approach for viral disease treatment. CRISPR/Cas9 is a specialised, effective, and adaptive gene-editing technique that can be used to modify, delete, or correct specific DNA sequences. It has evolved into an advanced, configurable nuclease-based single or multiple gene-editing tool with a wide range of applications. It is widely preferred simply because its operational procedures are simple, inexpensive, and extremely efficient. Exploration of infectious virus genomes is required for a comprehensive study of infectious viruses. Herein, we have discussed the historical timeline-based advancement of CRISPR, CRISPR/Cas9 as a gene-editing technology, the structure of CRISPR, and CRISPR as a diagnostic tool for studying emerging viral infections. Additionally, utilizing CRISPR/Cas9 technology to fight viral infections in plants, CRISPR-based diagnostics of viruses, pros, and cons, and bioethical issues of CRISPR/Cas9-based genomic modification are discussed.
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Affiliation(s)
- Shyam Tripathi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Purnima Khatri
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Zeeshan Fatima
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Correspondence: (R.P.P.); (S.H.)
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
- Correspondence: (R.P.P.); (S.H.)
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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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32
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Robertson G, Burger J, Campa M. CRISPR/Cas-based tools for the targeted control of plant viruses. MOLECULAR PLANT PATHOLOGY 2022; 23:1701-1718. [PMID: 35920132 PMCID: PMC9562834 DOI: 10.1111/mpp.13252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 05/15/2023]
Abstract
Plant viruses are known to infect most economically important crops and pose a major threat to global food security. Currently, few resistant host phenotypes have been delineated, and while chemicals are used for crop protection against insect pests and bacterial or fungal diseases, these are inefficient against viral diseases. Genetic engineering emerged as a way of modifying the plant genome by introducing functional genes in plants to improve crop productivity under adverse environmental conditions. Recently, new breeding technologies, and in particular the exciting CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) technology, was shown to be a powerful alternative to engineer resistance against plant viruses, thus has great potential for reducing crop losses and improving plant productivity to directly contribute to food security. Indeed, it could circumvent the "Genetic modification" issues because it allows for genome editing without the integration of foreign DNA or RNA into the genome of the host plant, and it is simpler and more versatile than other new breeding technologies. In this review, we describe the predominant features of the major CRISPR/Cas systems and outline strategies for the delivery of CRISPR/Cas reagents to plant cells. We also provide an overview of recent advances that have engineered CRISPR/Cas-based resistance against DNA and RNA viruses in plants through the targeted manipulation of either the viral genome or susceptibility factors of the host plant genome. Finally, we provide insight into the limitations and challenges that CRISPR/Cas technology currently faces and discuss a few alternative applications of the technology in virus research.
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Affiliation(s)
- Gaëlle Robertson
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
- Department of Experimental and Health SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Johan Burger
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
| | - Manuela Campa
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
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Justine AK, Kaur N, Savita, Pati PK. Biotechnological interventions in banana: current knowledge and future prospects. Heliyon 2022; 8:e11636. [DOI: 10.1016/j.heliyon.2022.e11636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/01/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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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: 26] [Impact Index Per Article: 13.0] [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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36
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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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Talakayala A, Mekala GK, Reddy MK, Ankanagari S, Garladinne M. Manipulating resistance to mungbean yellow mosaic virus in greengram (Vigna radiata L): Through CRISPR/Cas9 mediated editing of the viral genome. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.911574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) associated protein (CRISPR/Cas9) is an adaptive immune system of bacteria to counter the impending viral pathogen attack. With persistent improvements, CRISPR has become a versatile tool for developing molecular immunity against viruses in plants. In the current report, we utilized the Cas9 endonuclease and dual 20 bp-gRNAs targeting two different locations in single-stranded DNA-A of AC1 (rep protein) and AV1 (coat protein) of mungbean yellow mosaic virus for achieving resistance in greengram. The cotyledonary nodal explants were infected with Agrobacterium strain EHA105 harboring pMDC100-Cas9 with AC1 and AV1 gRNA cassettes and generated transgenic plants. The integration of Cas9 and gRNA cassettes in the transformed plants of greengram were confirmed by PCR and dot blot assays. Agroinfiltrated T2 transgenic lines exhibited minimal mosaic symptoms. A drastic reduction in the accumulation of AC1 and AV1 was observed in T2 transformed lines. The T7EI assay indicated that AC1 fragments were edited at a frequency of 46%, 32%, 20%, and AV1 at 38.15%, 40%, and 21.36% in MYMV infected greengram lines T2-6-2-3, T2-6-4-4, and T2-6-4-7, respectively. The manipulation of resistance to MYMV through the editing of the pathogen genome using the CRISPR/Cas9 tool can be a powerful approach to combat viruses and develop resistance in greengram.
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Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [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: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
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40
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Subrahmanyeswari T, Gantait S. Biotechnology of banana (Musa spp.): multi-dimensional progress and prospect of in vitro-mediated system. Appl Microbiol Biotechnol 2022; 106:3923-3947. [PMID: 35616721 DOI: 10.1007/s00253-022-11973-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
Abstract
Banana (Musa spp.), commonly known as 'Adam fig' and 'Fruit of wise man', is a commercial herbaceous tropical fruit, which governs its antiquity from ancient periods in the Indian and African subcontinent. All parts of the plant, i.e. stem, leaf, root, inflorescence, peel, fruit, and flower, have significant medicinal and nutritional values. Owing to its multitude of uses, it is known as 'Kalpavriksha' (plant of virtues). To combat multi-faceted issues related to traditional propagation, in vitro-based regeneration-cum-genetic improvement approaches become the trend of the hour. The present review illustrates various physico-chemical factors that are responsible for successful in vitro regeneration and acclimatization, protoplast culture, anther and microspore culture, cryopreservation and synthetic seed production, genetic transformation, mutagenesis, and nanotechnological and omics approaches. The key intent of this article is to present an insight on in vitro biotechnological research advances in the past decade, to identify the research gaps, unexplored areas, and major shortcomings associated with banana biotechnology and to highlight the potential approaches to mitigate them. Eventually, this review made salient conclusions and recommendations paving the way forward for the banana researchers to develop innovative ideas in order to enhance the propagation frequency and to ensure the genetic improvement of banana. KEY POINTS: • This review addresses biotechnological interventions in Banana (Musa spp.) for enhanced propagation and quality improvement. • Highlights factors influencing in vitro regeneration, conservation, and genetic transformation. • Provides novel ideas to harness the qualitative and quantitative genetic improvement.
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Affiliation(s)
- Tsama Subrahmanyeswari
- Crop Research Unit (Genetics and Plant Breeding), Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741252, India
| | - Saikat Gantait
- Crop Research Unit (Genetics and Plant Breeding), Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741252, India.
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41
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Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World. PLANTS 2022; 11:plants11101297. [PMID: 35631721 PMCID: PMC9146367 DOI: 10.3390/plants11101297] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022]
Abstract
Technological applications in agriculture have evolved substantially to increase crop yields and quality to meet global food demand. Conventional techniques, such as seed saving, selective breeding, and mutation breeding (variation breeding), have dramatically increased crop production, especially during the ‘Green Revolution’ in the 1990s. However, newer issues, such as limited arable lands, climate change, and ever-increasing food demand, pose challenges to agricultural production and threaten food security. In the following ‘Gene Revolution’ era, rapid innovations in the biotechnology field provide alternative strategies to further improve crop yield, quality, and resilience towards biotic and abiotic stresses. These innovations include the introduction of DNA recombinant technology and applications of genome editing techniques, such as transcription activator-like effector (TALEN), zinc-finger nucleases (ZFN), and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas) systems. However, the acceptance and future of these modern tools rely on the regulatory frameworks governing their development and production in various countries. Herein, we examine the evolution of technological applications in agriculture, focusing on the motivations for their introduction, technical challenges, possible benefits and concerns, and regulatory frameworks governing genetically engineered product development and production.
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42
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- *Correspondence: Leena Tripathi,
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Silva G, Bömer M, Turaki AA, Nkere CK, Kumar PL, Seal SE. Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:846989. [PMID: 35620696 PMCID: PMC9127665 DOI: 10.3389/fpls.2022.846989] [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: 12/31/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Aliyu A. Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | - Chukwuemeka K. Nkere
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Crop Protection and Environmental Biology (CPEB), University of Ibadan, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
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Mertens A, Bawin Y, Vanden Abeele S, Kallow S, Swennen R, Vu DT, Vu TD, Minh HT, Panis B, Vandelook F, Janssens SB. Phylogeography and conservation gaps of Musa balbisiana Colla genetic diversity revealed by microsatellite markers. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2515-2534. [PMID: 36017134 PMCID: PMC9393128 DOI: 10.1007/s10722-022-01389-4] [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: 11/05/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10722-022-01389-4.
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Affiliation(s)
- Arne Mertens
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Yves Bawin
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Simon Kallow
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly, UK
| | - Rony Swennen
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
- Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tuong Dang Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ho Thi Minh
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Bart Panis
- Bioversity International, Leuven, Belgium
| | | | - Steven B. Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
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45
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Aesaert S, Impens L, Coussens G, Van Lerberge E, Vanderhaeghen R, Desmet L, Vanhevel Y, Bossuyt S, Wambua AN, Van Lijsebettens M, Inzé D, De Keyser E, Jacobs TB, Karimi M, Pauwels L. Optimized Transformation and Gene Editing of the B104 Public Maize Inbred by Improved Tissue Culture and Use of Morphogenic Regulators. FRONTIERS IN PLANT SCIENCE 2022; 13:883847. [PMID: 35528934 PMCID: PMC9072829 DOI: 10.3389/fpls.2022.883847] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/22/2022] [Indexed: 05/13/2023]
Abstract
Plant transformation is a bottleneck for the application of gene editing in plants. In Zea mays (maize), a breakthrough was made using co-transformation of the morphogenic transcription factors BABY BOOM (BBM) and WUSCHEL (WUS) to induce somatic embryogenesis. Together with adapted tissue culture media, this was shown to increase transformation efficiency significantly. However, use of the method has not been reported widely, despite a clear need for increased transformation capacity in academic settings. Here, we explore use of the method for the public maize inbred B104 that is widely used for transformation by the research community. We find that only modifying tissue culture media already boosts transformation efficiency significantly and can reduce the time in tissue culture by 1 month. On average, production of independent transgenic plants per starting embryo increased from 1 to 4% using BIALAPHOS RESISTANCE (BAR) as a selection marker. In addition, we reconstructed the BBM-WUS morphogenic gene cassette and evaluated its functionality in B104. Expression of the morphogenic genes under tissue- and development stage-specific promoters led to direct somatic embryo formation on the scutellum of zygotic embryos. However, eight out of ten resulting transgenic plants showed pleiotropic developmental defects and were not fertile. This undesirable phenotype was positively correlated with the copy number of the morphogenic gene cassette. Use of constructs in which morphogenic genes are flanked by a developmentally controlled Cre/LoxP recombination system led to reduced T-DNA copy number and fertile T0 plants, while increasing transformation efficiency from 1 to 5% using HIGHLY-RESISTANT ACETOLACTATE SYNTHASE as a selection marker. Addition of a CRISPR/Cas9 module confirmed functionality for gene editing applications, as exemplified by editing the gene VIRESCENT YELLOW-LIKE (VYL) that can act as a visual marker for gene editing in maize. The constructs, methods, and insights produced in this work will be valuable to translate the use of BBM-WUS and other emerging morphogenic regulators (MRs) to other genotypes and crops.
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Affiliation(s)
- Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lennert Impens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Els Van Lerberge
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rudy Vanderhaeghen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurence Desmet
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Yasmine Vanhevel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shari Bossuyt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Angeline Ndele Wambua
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ellen De Keyser
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Thomas B. Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Mansour Karimi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Sturme MHJ, van der Berg JP, Bouwman LMS, De Schrijver A, de Maagd RA, Kleter GA, Battaglia-de Wilde E. Occurrence and Nature of Off-Target Modifications by CRISPR-Cas Genome Editing in Plants. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2022; 2:192-201. [PMID: 35548699 PMCID: PMC9075866 DOI: 10.1021/acsagscitech.1c00270] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022]
Abstract
![]()
CRISPR-Cas-based
genome editing allows for precise and targeted
genetic modification of plants. Nevertheless, unintended off-target
edits can arise that might confer risks when present in gene-edited
food crops. Through an extensive literature review we gathered information
on CRISPR-Cas off-target edits in plants. Most observed off-target
changes were small insertions or deletions (1–22 bp) or nucleotide
substitutions, and large deletions (>100 bp) were rare. One study
detected the insertion of vector-derived DNA sequences, which is important
considering the risk assessment of gene-edited plants. Off-target
sites had few mismatches (1–3 nt) with the target sequence
and were mainly located in protein-coding regions, often in target
gene homologues. Off-targets edits were predominantly detected via
biased analysis of predicted off-target sites instead of unbiased
genome-wide analysis. CRISPR-Cas-edited plants showed lower off-target
mutation frequencies than conventionally bred plants. This Review
can aid discussions on the relevance of evaluating off-target modifications
for risk assessment of CRISPR-Cas-edited plants.
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Affiliation(s)
- Mark H J Sturme
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Jan Pieter van der Berg
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Lianne M S Bouwman
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Ruud A de Maagd
- Wageningen Plant Research, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Gijs A Kleter
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Evy Battaglia-de Wilde
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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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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48
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Sharma P, Singh SP, Iqbal HM, Parra-Saldivar R, Varjani S, Tong YW. Genetic modifications associated with sustainability aspects for sustainable developments. Bioengineered 2022; 13:9508-9520. [PMID: 35389819 PMCID: PMC9161841 DOI: 10.1080/21655979.2022.2061146] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Sustainable development serves as the foundation for a range of international and national policymaking. Traditional breeding methods have been used to modify plant genomes and production. Genetic engineering is the practice of assisting agricultural systems in adapting to rapidly changing global growth by hastening the breeding of new varieties. On the other hand, the development of genetic engineering has enabled more precise control over the genomic alterations made in recent decades. Genetic changes from one species can now be introduced into a completely unrelated species, increasing agricultural output or making certain elements easier to manufacture. Harvest plants and soil microorganisms are just a few of the more well-known genetically modified creatures. Researchers assess current studies and illustrate the possibility of genetically modified organisms (GMOs) from the perspectives of various stakeholders. GMOs increase yields, reduce costs, and reduce agriculture's terrestrial and ecological footprint. Modern technology benefits innovators, farmers, and consumers alike. Agricultural biotechnology has numerous applications, each with its own set of potential consequences. This will be able to reach its full potential if more people have access to technology and excessive regulation is avoided. This paper covers the regulations for genetically modified crops (GMCs) as well as the economic implications. It also includes sections on biodiversity and environmental impact, as well as GMCs applications. This recounts biotechnological interventions for long-term sustainability in the field of GMCs, as well as the challenges and opportunities in this field of research.Abbreviations: GMCs-Genetically modified crops; GMOs- Genetically modified organisms; GE- Genetic engineering; Bt- Bacillus thuringiensisNIH- National Institutes of Health; FDA- Food and Drug Administration; HGT- Horizontal gene transfer; GM- Genetically modified; rDNA- Ribosomal deoxyribonucleic acid; USDA- United States Department of Agriculture; NIH- National Institutes of Health.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, Singapore
- Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, D.A.V. College, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Roberto Parra-Saldivar
- FEMSA, Tecnológico de MonterreyEscuela de Ingeniería y Ciencias- Centro de Biotecnología-, Monterrey, Mexico
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, India
- CONTACT Sunita Varjani ; Yen Wah Tong Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, Singapore
- Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
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49
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Control of Bacterial Diseases of Banana Using CRISPR/Cas-Based Gene Editing. Int J Mol Sci 2022; 23:ijms23073619. [PMID: 35408979 PMCID: PMC8998688 DOI: 10.3390/ijms23073619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/30/2022] Open
Abstract
Banana is an important staple food crop and a source of income for smallholder farmers in about 150 tropical and sub-tropical countries. Several bacterial diseases, such as banana Xanthomonas wilt (BXW), blood, and moko disease, cause substantial impacts on banana production. There is a vast yield gap in the production of bananas in regions where bacterial pathogens and several other pathogens and pests are present together in the same field. BXW disease caused by Xanthomonas campestris pv. musacearum is reported to be the most destructive banana disease in East Africa. The disease affects all the banana varieties grown in the region. Only the wild-type diploid banana, Musa balbisiana, is resistant to BXW disease. Developing disease-resistant varieties of bananas is one of the most effective strategies to manage diseases. Recent advances in CRISPR/Cas-based gene editing techniques can accelerate banana improvement. Some progress has been made to create resistance against bacterial pathogens using CRISPR/Cas9-mediated gene editing by knocking out the disease-causing susceptibility (S) genes or activating the expression of the plant defense genes. A synopsis of recent advancements and perspectives on the application of gene editing for the control of bacterial wilt diseases are presented in this article.
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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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