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Inam S, Muhammad A, Irum S, Rehman N, Riaz A, Uzair M, Khan MR. Genome editing for improvement of biotic and abiotic stress tolerance in cereals. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24092. [PMID: 39222468 DOI: 10.1071/fp24092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems.
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Affiliation(s)
- Safeena Inam
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Amna Muhammad
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Samra Irum
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Nazia Rehman
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Aamir Riaz
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Uzair
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Ramzan Khan
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
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Rashid A, Achary VMM, Abdin MZ, Karippadakam S, Parmar H, Panditi V, Prakash G, Bhatnagar-Mathur P, Reddy MK. Cytokinin oxidase2-deficient mutants improve panicle and grain architecture through cytokinin accumulation and enhance drought tolerance in indica rice. PLANT CELL REPORTS 2024; 43:207. [PMID: 39096362 DOI: 10.1007/s00299-024-03289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/16/2024] [Indexed: 08/05/2024]
Abstract
KEY MESSAGE The Osckx2 mutant accumulates cytokinin thereby enhancing panicle branching, grain yield, and drought tolerance, marked by improved survival rate, membrane integrity, and photosynthetic function. Cytokinins (CKs) are multifaceted hormones that regulate growth, development, and stress responses in plants. Cytokinins have been implicated in improved panicle architecture and grain yield; however, they are inactivated by the enzyme cytokinin oxidase (CKX). In this study, we developed a cytokinin oxidase 2 (Osckx2)-deficient mutant using CRISPR/Cas9 gene editing in indica rice and assessed its function under water-deficit and salinity conditions. Loss of OsCKX2 function increased grain number, secondary panicle branching, and overall grain yield through improved cytokinin content in the panicle tissue. Under drought conditions, the Osckx2 mutant conserved more water and demonstrated improved water-saving traits. Through reduced transpiration, Osckx2 mutants showed an improved survival response than the wild type to unset dehydration stress. Further, Osckx2 maintained chloroplast and membrane integrity and showed significantly improved photosynthetic function under drought conditions through enhanced antioxidant protection systems. The OsCKX2 function negatively affects panicle grain number and drought tolerance, with no discernible impact in response to salinity. The finding suggests the utility of the beneficial Osckx2 allele in breeding to develop climate-resilient, high-yielding cultivars for future food security.
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Affiliation(s)
- Afreen Rashid
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067
- Department of Biotechnology, Centre for Transgenic Plant Development, Jamia Hamdard, New Delhi, India, 110062
| | - V Mohan M Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067.
| | - M Z Abdin
- Department of Biotechnology, Centre for Transgenic Plant Development, Jamia Hamdard, New Delhi, India, 110062
| | - Sangeetha Karippadakam
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067
| | - Hemangini Parmar
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067
| | - Varakumar Panditi
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067
| | - Ganesan Prakash
- Plant Pathology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India, 110012
| | - Pooja Bhatnagar-Mathur
- Plant Breeding and Genetics, International Atomic Energy Agency (IAEA), PO-1001400, Vienna, Austria
| | - Malireddy K Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, Delhi, India, 110067
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Mishra S, Nayak S, Tuteja N, Poosapati S, Swain DM, Sahoo RK. CRISPR/Cas-Mediated Genome Engineering in Plants: Application and Prospectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1884. [PMID: 39065411 PMCID: PMC11279650 DOI: 10.3390/plants13141884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Genetic engineering has become an essential element in developing climate-resilient crops and environmentally sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition-rich, disease-resistant, and stress-tolerant "crops", fruits, and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different aspects of stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign-DNA-free or non-transgenic crops that could be easily regulated for commercialization in most countries.
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Affiliation(s)
- Swetaleena Mishra
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, India;
| | - Subhendu Nayak
- Vidya USA Corporation, Otis Stone Hunter Road, Bunnell, FL 32100, USA;
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India;
| | - Sowmya Poosapati
- Plant Biology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92037, USA
| | - Durga Madhab Swain
- MU Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, India;
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Elsisi M, Elshiekh M, Sabry N, Aziz M, Attia K, Islam F, Chen J, Abdelrahman M. The genetic orchestra of salicylic acid in plant resilience to climate change induced abiotic stress: critical review. STRESS BIOLOGY 2024; 4:31. [PMID: 38880851 PMCID: PMC11180647 DOI: 10.1007/s44154-024-00160-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/12/2024] [Indexed: 06/18/2024]
Abstract
Climate change, driven by human activities and natural processes, has led to critical alterations in varying patterns during cropping seasons and is a vital threat to global food security. The climate change impose several abiotic stresses on crop production systems. These abiotic stresses include extreme temperatures, drought, and salinity, which expose agricultural fields to more vulnerable conditions and lead to substantial crop yield and quality losses. Plant hormones, especially salicylic acid (SA), has crucial roles for plant resiliency under unfavorable environments. This review explores the genetics and molecular mechanisms underlying SA's role in mitigating abiotic stress-induced damage in plants. It also explores the SA biosynthesis pathways, and highlights the regulation of their products under several abiotic stresses. Various roles and possible modes of action of SA in mitigating abiotic stresses are discussed, along with unraveling the genetic mechanisms and genes involved in responses under stress conditions. Additionally, this review investigates molecular pathways and mechanisms through which SA exerts its protective effects, such as redox signaling, cross-talks with other plant hormones, and mitogen-activated protein kinase pathways. Moreover, the review discusses potentials of using genetic engineering approaches, such as CRISPR technology, for deciphering the roles of SA in enhancing plant resilience to climate change related abiotic stresses. This comprehensive analysis bridges the gap between genetics of SA role in response to climate change related stressors. Overall goal is to highlight SA's significance in safeguarding plants and by offering insights of SA hormone for sustainable agriculture under challenging environmental conditions.
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Affiliation(s)
- Mohamed Elsisi
- School of Biotechnology, Nile University, Giza, 12588, Egypt
| | - Moaz Elshiekh
- School of Biotechnology, Nile University, Giza, 12588, Egypt
| | - Nourine Sabry
- School of Biotechnology, Nile University, Giza, 12588, Egypt
| | - Mark Aziz
- School of Biotechnology, Nile University, Giza, 12588, Egypt
| | - Kotb Attia
- College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Faisal Islam
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China.
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China.
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Hwarari D, Radani Y, Ke Y, Chen J, Yang L. CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks. Funct Integr Genomics 2024; 24:50. [PMID: 38441816 DOI: 10.1007/s10142-024-01314-1] [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: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
The CRISPR/Cas systems have emerged as transformative tools for precisely manipulating plant genomes and enhancement. It has provided unparalleled applications from modifying the plant genomes to resistant enhancement. This review manuscript summarises the mechanism, application, and current challenges in the CRISPR/Cas genome editing technology. It addresses the molecular mechanisms of different Cas genes, elucidating their applications in various plants through crop improvement, disease resistance, and trait improvement. The advent of the CRISPR/Cas systems has enabled researchers to precisely modify plant genomes through gene knockouts, knock-ins, and gene expression modulation. Despite these successes, the CRISPR/Cas technology faces challenges, including off-target effects, Cas toxicity, and efficiency. In this manuscript, we also discuss these challenges and outline ongoing strategies employed to overcome these challenges, including the development of novel CRISPR/Cas variants with improved specificity and specific delivery methods for different plant species. The manuscript will conclude by addressing the future perspectives of the CRISPR/Cas technology in plants. Although this review manuscript is not conclusive, it aims to provide immense insights into the current state and future potential of CRISPR/Cas in sustainable and secure plant production.
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Affiliation(s)
- Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongchao Ke
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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Kappachery S, AlHosani M, Khan TA, AlKharoossi SN, AlMansoori N, AlShehhi SAS, AlMansoori H, AlKarbi M, Sasi S, Karumannil S, Elangovan SK, Shah I, Gururani MA. Modulation of antioxidant defense and PSII components by exogenously applied acetate mitigates salinity stress in Avena sativa. Sci Rep 2024; 14:620. [PMID: 38182773 PMCID: PMC10770181 DOI: 10.1038/s41598-024-51302-5] [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: 09/26/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
Salinity stress has detrimental effects on various aspects of plant development. However, our understanding of strategies to mitigate these effects in crop plants remains limited. Recent research has shed light on the potential of sodium acetate as a mitigating component against salinity stress in several plant species. Here, we show the role of acetate sodium in counteracting the adverse effects on oat (Avena sativa) plants subjected to NaCl-induced salinity stress, including its impact on plant morphology, photosynthetic parameters, and gene expression related to photosynthesis and antioxidant capacity, ultimately leading to osmoprotection. The five-week experiment involved subjecting oat plants to four different conditions: water, salt (NaCl), sodium acetate, and a combination of salt and sodium acetate. The presence of NaCl significantly inhibited plant growth and root elongation, disrupted chlorophylls and carotenoids content, impaired chlorophyll fluorescence, and down-regulated genes associated with the plant antioxidant defense system. Furthermore, our findings reveal that when stressed plants were treated with sodium acetate, it partially reversed these adverse effects across all analyzed parameters. This reversal was particularly evident in the increased content of proline, thereby ensuring osmoprotection for oat plants, even under stressful conditions. These results provide compelling evidence regarding the positive impact of sodium acetate on various plant development parameters, with a particular focus on the enhancement of photosynthetic activity.
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Affiliation(s)
- Sajeesh Kappachery
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Mohamed AlHosani
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Tanveer Alam Khan
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Sara Nouh AlKharoossi
- Department of Chemistry, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Nemah AlMansoori
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Sara Ali Saeed AlShehhi
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Hamda AlMansoori
- Department of Chemistry, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Maha AlKarbi
- Department of Chemistry, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Sameera Karumannil
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Sampath Kumar Elangovan
- Department of Chemistry, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Iltaf Shah
- Department of Chemistry, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE
| | - Mayank Anand Gururani
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al Ain, UAE.
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Matinvafa MA, Makani S, Parsasharif N, Zahed MA, Movahed E, Ghiasvand S. CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology. 3 Biotech 2023; 13:383. [PMID: 37920190 PMCID: PMC10618153 DOI: 10.1007/s13205-023-03786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/09/2023] [Indexed: 11/04/2023] Open
Abstract
The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.
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Affiliation(s)
- Mohammad Ali Matinvafa
- Department of Biotechnology & Environment, Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Shadi Makani
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Negin Parsasharif
- Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY USA
| | - Saeedeh Ghiasvand
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Hamedan, Iran
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. RICE (NEW YORK, N.Y.) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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Qing D, Chen W, Huang S, Li J, Pan Y, Zhou W, Liang Q, Yuan J, Gan D, Chen L, Chen L, Huang J, Zhou Y, Dai G, Deng G. Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components. Proteomics 2023; 23:e2200538. [PMID: 37376803 DOI: 10.1002/pmic.202200538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Grain size is one of the most important agronomic traits for grain yield determination in rice. To better understand the proteins that are regulated by the grain size regulatory gene OsMKK3, this gene was knocked out using the CRISPR/Cas9 system, and tandem mass tag (TMT) labeling combined with liquid chromatograph-tandem mass spectrometry analysis was performed to study the regulation of proteins in the panicle. Quantitative proteomic screening revealed a total of 106 differentially expressed proteins (DEPs) via comparison of the OsMKK3 mutant line to the wild-type YexiangB, including 15 and 91 up-regulated and down-regulated DEPs, respectively. Pathway analysis revealed that DEPs were enriched in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and photosynthesis. Strong interactions were detected among seven down-regulated proteins related to photosystem components in the protein-protein interaction network, and photosynthetic rate was decreased in mutant plants. The results of the liquid chromatography-parallel reaction monitoring/mass spectromery analysis and western blot analysis were consistent with the results of the proteomic analysis, and the results of the quantitative reverse transcription polymerase chain reaction analysis revealed that the expression levels of most candidate genes were consistent with protein levels. Overall, OsMKK3 controls grain size by regulating the protein content in cells. Our findings provide new candidate genes that will aid the study of grain size regulatory mechanisms associated with the mitogen-activated protein kinase (MAPK) signaling pathway.
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Affiliation(s)
- Dongjin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiwei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Suosheng Huang
- Guangxi Academy of Agricultural Sciences, Plant Protection Research Institute, Nanning, China
| | - Jingcheng Li
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yinghua Pan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiyong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Qiongyue Liang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Jinghua Yuan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Dongmei Gan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Li Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Lei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yan Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Gaoxing Dai
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Guofu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Chauhan S, Tiwari PN, Payasi DK. Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants. Life (Basel) 2023; 13:1456. [PMID: 37511831 PMCID: PMC10381907 DOI: 10.3390/life13071456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Genome editing aims to revolutionise plant breeding and could assist in safeguarding the global food supply. The inclusion of a 12-40 bp recognition site makes mega nucleases the first tools utilized for genome editing and first generation gene-editing tools. Zinc finger nucleases (ZFNs) are the second gene-editing technique, and because they create double-stranded breaks, they are more dependable and effective. ZFNs were the original designed nuclease-based approach of genome editing. The Cys2-His2 zinc finger domain's discovery made this technique possible. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, boost biomass production, increase nutrient usage efficiency, and develop disease resistance. Plant genomes can be effectively modified using genome-editing technologies to enhance characteristics without introducing foreign DNA into the genome. Next-generation plant breeding will soon be defined by these exact breeding methods. There is abroad promise that genome-edited crops will be essential in the years to come for improving the sustainability and climate-change resilience of food systems. This method also has great potential for enhancing crops' resistance to various abiotic stressors. In this review paper, we summarize the most recent findings about the mechanism of abiotic stress response in crop plants and the use of the CRISPR/Cas mediated gene-editing systems to improve tolerance to stresses including drought, salinity, cold, heat, and heavy metals.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Prakash Narayan Tiwari
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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13
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Rai GK, Khanday DM, Kumar P, Magotra I, Choudhary SM, Kosser R, Kalunke R, Giordano M, Corrado G, Rouphael Y, Pandey S. Enhancing Crop Resilience to Drought Stress through CRISPR-Cas9 Genome Editing. PLANTS (BASEL, SWITZERLAND) 2023; 12:2306. [PMID: 37375931 DOI: 10.3390/plants12122306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
With increasing frequency and severity of droughts in various parts of the world, agricultural productivity may suffer major setbacks. Among all the abiotic factors, drought is likely to have one of the most detrimental effects on soil organisms and plants. Drought is a major problem for crops because it limits the availability of water, and consequently nutrients which are crucial for plant growth and survival. This results in reduced crop yields, stunted growth, and even plant death, according to the severity and duration of the drought, the plant's developmental stage, and the plant's genetic background. The ability to withstand drought is a highly complex characteristic that is controlled by multiple genes, making it one of the most challenging attributes to study, classify, and improve. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) technology has opened a new frontier in crop enhancement, revolutionizing plant molecular breeding. The current review provides a general understanding of principles as well as optimization of CRISPR system, and presents applications on genetic enhancement of crops, specifically in terms of drought resistance and yield. Moreover, we discuss how innovative genome editing techniques can aid in the identification and modification of genes conferring drought tolerance.
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Affiliation(s)
- Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Danish Mushtaq Khanday
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Pradeep Kumar
- Division of Integrated Farming System, ICAR-Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Isha Magotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Sadiya M Choudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Rafia Kosser
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Raviraj Kalunke
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Maria Giordano
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Sudhakar Pandey
- Indian Council of Agricultural Research, Krishi Anusandhan Bhavan II, New Delhi 110012, India
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14
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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15
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Wang Y, Wu F, Lin Q, Sheng P, Wu Z, Jin X, Chen W, Li S, Luo S, Duan E, Wang J, Ma W, Ren Y, Cheng Z, Zhang X, Lei C, Guo X, Wang H, Zhu S, Wan J. A regulatory loop establishes the link between the circadian clock and abscisic acid signaling in rice. PLANT PHYSIOLOGY 2023; 191:1857-1870. [PMID: 36493391 PMCID: PMC10022614 DOI: 10.1093/plphys/kiac548] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress responses. However, the exact feedback regulation mechanism between them is still poorly understood. Here, we identified the rice (Oryza sativa) clock component PSEUDO-RESPONSE REGULATOR 95 (OsPRR95) as a transcriptional regulator that accelerates seed germination and seedling growth by inhibiting ABA signaling. We also found that OsPRR95 binds to the ABA receptor gene REGULATORY COMPONENTS OF ABA RECEPTORS10 (OsRCAR10) DNA and inhibits its expression. Genetic analysis showed OsRCAR10 acts downstream of OsPRR95 in mediating ABA responses. In addition, the induction of OsPRR95 by ABA partly required a functional OsRCAR10, and the ABA-responsive element-binding factor ABSCISIC ACID INSENSITIVE5 (OsABI5) bound directly to the promoter of OsPRR95 and activated its expression, thus establishing a regulatory feedback loop between OsPRR95, OsRCAR10, and OsABI5. Taken together, our results demonstrated that the OsRCAR10-OsABI5-OsPRR95 feedback loop modulates ABA signaling to fine-tune seed germination and seedling growth, thus establishing the molecular link between ABA signaling and the circadian clock.
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Affiliation(s)
- Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ziming Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xin Jin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Erchao Duan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiachang Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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16
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Wang L, Wang L, Tan M, Wang L, Zhao W, You J, Wang L, Yan X, Wang W. The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses. Biol Res 2023; 56:12. [PMID: 36922868 PMCID: PMC10018860 DOI: 10.1186/s40659-023-00424-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Drought stress has significantly hampered agricultural productivity worldwide and can also result in modifications to DNA methylation levels. However, the dynamics of DNA methylation and its association with the changes in gene transcription and alternative splicing (AS) under drought stress are unknown in linseed, which is frequently cultivated in arid and semiarid regions. RESULTS We analysed AS events and DNA methylation patterns in drought-tolerant (Z141) and drought-sensitive (NY-17) linseed under drought stress (DS) and repeated drought stress (RD) treatments. We found that the number of intron-retention (IR) and alternative 3' splice site (Alt3'SS) events were significantly higher in Z141 and NY-17 under drought stress. We found that the linseed response to the DS treatment was mainly regulated by transcription, while the response to the RD treatment was coregulated by transcription and AS. Whole genome-wide DNA methylation analysis revealed that drought stress caused an increase in the overall methylation level of linseed. Although we did not observe any correlation between differentially methylated genes (DMGs) and differentially spliced genes (DSGs) in this study, we found that the DSGs whose gene body region was hypermethylated in Z141 and hypomethylated in NY-17 were enriched in abiotic stress response Gene Ontology (GO) terms. This finding implies that gene body methylation plays an important role in AS regulation in some specific genes. CONCLUSION Our study is the first comprehensive genome-wide analysis of the relationship between linseed methylation changes and AS under drought and repeated drought stress. Our study revealed different interaction patterns between differentially expressed genes (DEGs) and DSGs under DS and RD treatments and differences between methylation and AS regulation in drought-tolerant and drought-sensitive linseed varieties. The findings will probably be of interest in the future. Our results provide interesting insights into the association between gene expression, AS, and DNA methylation in linseed under drought stress. Differences in these associations may account for the differences in linseed drought tolerance.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Meilian Tan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Zhao
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | | | - Xingchu Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China.
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17
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Nascimento FDS, Rocha ADJ, Soares JMDS, Mascarenhas MS, Ferreira MDS, Morais Lino LS, Ramos APDS, Diniz LEC, Mendes TADO, Ferreira CF, dos Santos-Serejo JA, Amorim EP. Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:305. [PMID: 36679018 PMCID: PMC9860801 DOI: 10.3390/plants12020305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 05/22/2023]
Abstract
Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.
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Affiliation(s)
| | - Anelita de Jesus Rocha
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | - Mileide dos Santos Ferreira
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
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18
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Li Q, Shen C, Zhang Y, Zhou Y, Niu M, Wang HL, Lian C, Tian Q, Mao W, Wang X, Liu C, Yin W, Xia X. PePYL4 enhances drought tolerance by modulating water-use efficiency and ROS scavenging in Populus. TREE PHYSIOLOGY 2023; 43:102-117. [PMID: 36074523 DOI: 10.1093/treephys/tpac106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the major limiting factors in the growth of terrestrial plants. Abscisic acid (ABA) and pyrabactin resistance 1/prabactin resistance-1 like/regulatory components of ABA receptors (PYR/PYL/RCARs) play a key role in response to drought stress. However, the underlying mechanisms of this control remain largely elusive in trees. In this study, PePYL4, a potential ortholog of the PYR/PYL/RCARs gene, was cloned from Populus euphratica. It was localized in the cytoplasm and nucleus, induced by ABA, osmotic and dehydration treatments. To study the potential biological functions of PePYL4, transgenic triploid white poplars (Populus tomentosa 'YiXianCiZhu B38') overexpressing PePYL4 were generated. PePYL4 overexpression significantly increased ABA sensitivity and reduced stomatal aperture. Compared with wild-type plants, transgenic plants had higher water-use efficiency (WUE) and lower transpiration. When exposed to drought stress, PePYL4 overexpression plants maintained higher photosynthetic activity and accumulated more biomass. Moreover, overexpression of PePYL4 improved antioxidant enzyme activity and ascorbate content to accelerate reactive oxygen species scavenging. Meanwhile, upregulation expression of the stress-related genes also contributed to improving the drought tolerance of transgenic plants. In conclusion, our data suggest that PePYL4 is a promising gene target for regulating WUE and drought tolerance in Populus.
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Affiliation(s)
- Qing Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Chao Shen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yue Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yangyan Zhou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mengxue Niu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conglong Lian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianqian Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Mao
- Salver Academy of Botany, Rizhao 262305, China
| | | | - Chao Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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19
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Maharajan T, Chellasamy G, Tp AK, Ceasar SA, Yun K. The role of metal transporters in phytoremediation: A closer look at Arabidopsis. CHEMOSPHERE 2023; 310:136881. [PMID: 36257391 DOI: 10.1016/j.chemosphere.2022.136881] [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: 07/20/2022] [Revised: 09/26/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Pollution of the environment by heavy metals (HMs) has recently become a global issue, affecting the health of all living organisms. Continuous human activities (industrialization and urbanization) are the major causes of HM release into the environment. Over the years, two methods (physical and chemical) have been widely used to reduce HMs in polluted environment. However, these two methods are inefficient and very expensive to reduce the HMs released into the atmosphere. Alternatively, researchers are trying to remove the HMs by employing hyper-accumulator plants. This method, referred to phytoremediation, is highly efficient, cost-effective, and eco-friendly. Phytoremediation can be divided into five types: phytostabilization, phytodegradation, rhizofiltration, phytoextraction, and phytovolatilization, all of which contribute to HMs removal from the polluted environment. Brassicaceae family members (particularly Arabidopsis thaliana) can accumulate more HMs from the contaminated environment than those of other plants. This comprehensive review focuses on how HMs pollute the environment and discusses the phytoremediation measures required to reduce the impact of HMs on the environment. We discuss the role of metal transporters in phytoremediation with a focus on Arabidopsis. Then draw insights into the role of genome editing tools in enhancing phytoremediation efficiency. This review is expected to initiate further research to improve phytoremediation by biotechnological approaches to conserve the environment from pollution.
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Affiliation(s)
- Theivanayagam Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Cochin, 683 104, Kerala, India
| | - Gayathri Chellasamy
- Department of Bionanotechnology, Gachon University, Gyeonggi-do, 13120, Republic of Korea
| | - Ajeesh Krishna Tp
- Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Cochin, 683 104, Kerala, India
| | - Stanislaus Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Cochin, 683 104, Kerala, India.
| | - Kyusik Yun
- Department of Bionanotechnology, Gachon University, Gyeonggi-do, 13120, Republic of Korea.
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Wang C, Gao B, Chen N, Jiao P, Jiang Z, Zhao C, Ma Y, Guan S, Liu S. A Novel Senescence-Specific Gene ( ZmSAG39) Negatively Regulates Darkness and Drought Responses in Maize. Int J Mol Sci 2022; 23:15984. [PMID: 36555622 PMCID: PMC9785699 DOI: 10.3390/ijms232415984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The papain-like cysteine proteases (PLCPs) is a subfamily of cysteine proteases that plays an important role in leaf senescence, and some of its members are involved in the regulation of plant growth and development under stress. In this study, we cloned a new gene, ZmSAG39, from maize. Expression profile analysis showed that ZmSAG39 was induced by darkness and drought treatments. In addition, the ZmSAG39 overexpression in maize accelerated the senescence of maize leaves under darkness and drought treatments. However, the knockout of ZmSAG39 in maize enhanced the resistance of maize to darkness and drought stresses and reduced the degree of senescence of maize leaves. Under drought stress, compared with WT plants, the knockout lines had a higher seed germination rate, seedling survival rate and chlorophyll content, and lower reactive oxygen species (ROS) level and malondialdehyde (MDA) content. In addition, quantitative real-time PCR (qRT-PCR) analysis showed that ZmSAG39 negatively regulated some stress-related genes but positively regulated senescence-related genes under darkness and drought stress conditions. To summarize, these results indicate that ZmSAG39 is a senescence-related gene and plays a negative role in response to darkness and drought stresses. This study laid a theoretical foundation for the innovation of maize germplasm resources with high quality, high yield and strong stress resistance.
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Affiliation(s)
- Chunlai Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Bai Gao
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Nannan Chen
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Peng Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Zhenzhong Jiang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Chunli Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Yiyong Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Shuyan Guan
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Siyan Liu
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
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21
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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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22
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Maharajan T, Krishna TPA, Rakkammal K, Ceasar SA, Ramesh M. Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance. PLANTA 2022; 256:106. [PMID: 36326904 DOI: 10.1007/s00425-022-04023-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.
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Affiliation(s)
- Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - T P Ajeesh Krishna
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India.
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
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23
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Kausar R, Wang X, Komatsu S. Crop Proteomics under Abiotic Stress: From Data to Insights. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212877. [PMID: 36365330 PMCID: PMC9657731 DOI: 10.3390/plants11212877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 06/09/2023]
Abstract
Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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24
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Villalobos-López MA, Arroyo-Becerra A, Quintero-Jiménez A, Iturriaga G. Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:12053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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Affiliation(s)
- Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Anareli Quintero-Jiménez
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
| | - Gabriel Iturriaga
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
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25
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Li Y, Wu X, Zhang Y, Zhang Q. CRISPR/Cas genome editing improves abiotic and biotic stress tolerance of crops. Front Genome Ed 2022; 4:987817. [PMID: 36188128 PMCID: PMC9524261 DOI: 10.3389/fgeed.2022.987817] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Abiotic stress such as cold, drought, saline-alkali stress and biotic stress including disease and insect pest are the main factors that affect plant growth and limit agricultural productivity. In recent years, with the rapid development of molecular biology, genome editing techniques have been widely used in botany and agronomy due to their characteristics of high efficiency, controllable and directional editing. Genome editing techniques have great application potential in breeding resistant varieties. These techniques have achieved remarkable results in resistance breeding of important cereal crops (such as maize, rice, wheat, etc.), vegetable and fruit crops. Among them, CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) provides a guarantee for the stability of crop yield worldwide. In this paper, the development of CRISRR/Cas and its application in different resistance breeding of important crops are reviewed, the advantages and importance of CRISRR/Cas technology in breeding are emphasized, and the possible problems are pointed out.
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Affiliation(s)
- Yangyang Li
- Hunan Tobacco Research Institute, Changsha, China
| | - Xiuzhe Wu
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Qiang Zhang, ; Yan Zhang,
| | - Qiang Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Qiang Zhang, ; Yan Zhang,
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26
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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27
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Liu L, Wang X, Chang C. Toward a smart skin: Harnessing cuticle biosynthesis for crop adaptation to drought, salinity, temperature, and ultraviolet stress. FRONTIERS IN PLANT SCIENCE 2022; 13:961829. [PMID: 35958191 PMCID: PMC9358614 DOI: 10.3389/fpls.2022.961829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Drought, salinity, extreme temperatures, and ultraviolet (UV) radiation are major environmental factors that adversely affect plant growth and crop production. As a protective shield covering the outer epidermal cell wall of plant aerial organs, the cuticle is mainly composed of cutin matrix impregnated and sealed with cuticular waxes, and greatly contributes to the plant adaption to environmental stresses. Past decades have seen considerable progress in uncovering the molecular mechanism of plant cutin and cuticular wax biosynthesis, as well as their important roles in plant stress adaptation, which provides a new direction to drive strategies for stress-resilient crop breeding. In this review, we highlighted the recent advances in cuticle biosynthesis in plant adaptation to drought, salinity, extreme temperatures, and UV radiation stress, and discussed the current status and future directions in harnessing cuticle biosynthesis for crop improvement.
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28
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Environmental Stress and Plants. Int J Mol Sci 2022; 23:ijms23105416. [PMID: 35628224 PMCID: PMC9141089 DOI: 10.3390/ijms23105416] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 12/24/2022] Open
Abstract
Land plants are constantly subjected to multiple unfavorable or even adverse environmental conditions. Among them, abiotic stresses (such as salt, drought, heat, cold, heavy metals, ozone, UV radiation, and nutrient deficiencies) have detrimental effects on plant growth and productivity and are increasingly important considering the direct or indirect effects of climate change. Plants respond in many ways to abiotic stresses, from gene expression to physiology, from plant architecture to primary, and secondary metabolism. These complex changes allow plants to tolerate and/or adapt to adverse conditions. The complexity of plant response can be further influenced by the duration and intensity of stress, the plant genotype, the combination of different stresses, the exposed tissue and cell type, and the developmental stage at which plants perceive the stress. It is therefore important to understand more about how plants perceive stress conditions and how they respond and adapt (both in natural and anthropogenic environments). These concepts were the basis of the Special Issue that International Journal of Molecular Sciences expressly addressed to the relationship between environmental stresses and plants and that resulted in the publication of 5 reviews and 38 original research articles. The large participation of several authors and the good number of contributions testifies to the considerable interest that the topic currently receives in the plant science community, especially in the light of the foreseeable climate changes. Here, we briefly summarize the contributions included in the Special Issue, both original articles categorized by stress type and reviews that discuss more comprehensive responses to various stresses.
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29
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PYR/PYL/RCAR Receptors Play a Vital Role in the Abscisic-Acid-Dependent Responses of Plants to External or Internal Stimuli. Cells 2022; 11:cells11081352. [PMID: 35456031 PMCID: PMC9028234 DOI: 10.3390/cells11081352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 01/17/2023] Open
Abstract
Abscisic acid (ABA) is a phytohormone that plays a key role in regulating several developmental processes as well as in response to stressful conditions such as drought. Activation of the ABA signaling cascade allows the induction of an appropriate physiological response. The basic components of the ABA signaling pathway have been recognized and characterized in recent years. Pyrabactin resistance, pyrabactin resistance-like, and the regulatory component of ABA receptors (PYR/PYL/RCAR) are the major components responsible for the regulation of the ABA signaling pathway. Here, we review recent findings concerning the PYR/PYL/RCAR receptor structure, function, and interaction with other components of the ABA signaling pathway as well as the termination mechanism of ABA signals in plant cells. Since ABA is one of the basic elements related to abiotic stress, which is increasingly common in the era of climate changes, understanding the perception and transduction of the signal related to this phytohormone is of paramount importance in further increasing crop tolerance to various stress factors.
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30
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Ajeesh Krishna TP, Maharajan T, Ceasar SA. Improvement of millets in the post-genomic era. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:669-685. [PMID: 35465206 PMCID: PMC8986959 DOI: 10.1007/s12298-022-01158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 05/16/2023]
Abstract
Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.
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Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
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31
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Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice. PLANTS 2022; 11:plants11040524. [PMID: 35214855 PMCID: PMC8875723 DOI: 10.3390/plants11040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022]
Abstract
Bi-allelic mutant lines induced by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems are important genetic materials. It is very important to establish a rapid and cheap method in identifying homozygous mutant plants from offspring segregation populations of bi-allelic mutant lines. In this study, the offspring genotypes of rice bi-allelic starch branching enzyme IIb mutant lines were identified using the allele specific PCR (AS-PCR) method. The target sequences of two alleles were aligned from their 5′ to 3′ ends, and the first different bases were used as the 3′ ends of mismatch primers. Another mismatched base was introduced at the third nucleotide from the 3′ end of mismatch primer. The PCR reaction mixture and amplification program were optimized according to the differences of mutation target sequence and mismatch primers. The offspring plant genotypes of bi-allelic mutant lines could be accurately identified using the amplified DNA fragments by agarose gel electrophoresis. This study could provide a method reference for the rapid screening of homozygous mutant plants from offspring segregation population of heterozygous and bi-allelic mutant lines.
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32
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Berrío RT, Nelissen H, Inzé D, Dubois M. Increasing yield on dry fields: molecular pathways with growing potential. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:323-341. [PMID: 34695266 PMCID: PMC7612350 DOI: 10.1111/tpj.15550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 05/02/2023]
Abstract
Drought stress constitutes one of the major constraints to agriculture all over the world, and its devastating effect is only expected to increase in the following years due to climate change. Concurrently, the increasing food demand in a steadily growing population requires a proportional increase in yield and crop production. In the past, research aimed to increase plant resilience to severe drought stress. However, this often resulted in stunted growth and reduced yield under favorable conditions or moderate drought. Nowadays, drought tolerance research aims to maintain plant growth and yield under drought conditions. Overall, recently deployed strategies to engineer drought tolerance in the lab can be classified into a 'growth-centered' strategy, which focuses on keeping growth unaffected by the drought stress, and a 'drought resilience without growth penalty' strategy, in which the main aim is still to boost drought resilience, while limiting the side effects on plant growth. In this review, we put the scope on these two strategies and some molecular players that were successfully engineered to generate drought-tolerant plants: abscisic acid, brassinosteroids, cytokinins, ethylene, ROS scavenging genes, strigolactones, and aquaporins. We discuss how these pathways participate in growth and stress response regulation under drought. Finally, we present an overview of the current insights and future perspectives in the development of new strategies to improve drought tolerance in the field.
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Affiliation(s)
- Rubén Tenorio Berrío
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Corresponding Author: Dirk Inzé VIB Center for Plant Systems Biology Ghent University, Department of Plant Biotechnology Technologiepark 71 B-9052 Ghent (Belgium) Tel.: +32 9 3313800; Fax: +32 9 3313809;
| | - Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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Siva N, Gupta S, Gupta A, Shukla JN, Malik B, Shukla N. Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer. 3 Biotech 2021; 11:146. [PMID: 33732568 PMCID: PMC7910401 DOI: 10.1007/s13205-021-02680-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
The development of genome-editing technologies in 1970s has discerned a new beginning in the field of science. Out of different genome-editing approaches such as Zing-finger nucleases, TALENs, and meganucleases, clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR/Cas9) is a recent and versatile technology that has the ability of making changes to the genome of different organisms with high specificity. Cancer is a complex process that is characterized by multiple genetic and epigenetic changes resulting in abnormal cell growth and proliferation. As cancer is one of the leading causes of deaths worldwide, a large number of studies are done to understand the molecular mechanisms underlying the development of cancer. Because of its high efficiency and specificity, CRISPR/Cas9 has emerged as a novel and powerful tool in the field of cancer research. CRISPR/Cas9 has the potential to accelerate cancer research by dissecting tumorigenesis process, generating animal and cellular models, and identify drug targets for chemotherapeutic approaches. However, despite having tremendous potential, there are certain challenges associated with CRISPR/Cas9 such as safe delivery to the target, potential off-target effects and its efficacy which needs to be addressed prior to its clinical application. In this review, we give a gist of different genome-editing technologies with a special focus on CRISPR/Cas9 development, its mechanism of action and its applications, especially in different type of cancers. We also highlight the importance of CRISPR/Cas9 in generating animal models of different cancers. Finally, we present an overview of the clinical trials and discuss the challenges associated with translating CRISPR/Cas9 in clinical use.
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Affiliation(s)
- Narmadhaa Siva
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Ayam Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer, India
| | - Babita Malik
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur, India
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
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Usman B, Nawaz G, Zhao N, Liao S, Qin B, Liu F, Liu Y, Li R. Programmed Editing of Rice ( Oryza sativa L.) OsSPL16 Gene Using CRISPR/Cas9 Improves Grain Yield by Modulating the Expression of Pyruvate Enzymes and Cell Cycle Proteins. Int J Mol Sci 2020; 22:E249. [PMID: 33383688 PMCID: PMC7795130 DOI: 10.3390/ijms22010249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/17/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the major crops in the world and significant increase in grain yield is constant demand for breeders to meet the needs of a rapidly growing population. The size of grains is one of major components determining rice yield and a vital trait for domestication and breeding. To increase the grain size in rice, OsSPL16/qGW8 was mutagenized through CRISPR/Cas9, and proteomic analysis was performed to reveal variations triggered by mutations. More specifically, mutants were generated with two separate guide RNAs targeting recognition sites on opposite strands and genomic insertions and deletions were characterized. Mutations followed Mendelian inheritance and homozygous and heterozygous mutants lacking any T-DNA and off-target effects were screened. The mutant lines showed a significant increase in grain yield without any change in other agronomic traits in T0, T1, and T2 generations. Proteomic screening found a total of 44 differentially expressed proteins (DEPs), out of which 33 and 11 were up and downregulated, respectively. Most of the DEPs related to pyruvate kinase, pyruvate dehydrogenase, and cell division and proliferation were upregulated in the mutant plants. Pathway analysis revealed that DEPs were enriched in the biosynthesis of secondary metabolites, pyruvate metabolism, glycolysis/gluconeogenesis, carbon metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and citrate cycle. Gene Ontology (GO) analysis presented that most of the DEPs were involved in the pyruvate metabolic process and pyruvate dehydrogenase complex. Proteins related to pyruvate dehydrogenase E1 component subunit alpha-1 displayed higher interaction in the protein-protein interaction (PPI) network. Thus, the overall results revealed that CRISPR/Cas9-guided OsSPL16 mutations have the potential to boost the grain yield of rice. Additionally, global proteome analysis has broad applications for discovering molecular components and dynamic regulation underlying the targeted gene mutations.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Shanyue Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
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