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Patra S, Chatterjee D, Basak S, Sen S, Mandal A. CRISPR/Cas9 opens new horizon of crop improvement under stress condition. Biochim Biophys Acta Gen Subj 2024; 1868:130685. [PMID: 39079650 DOI: 10.1016/j.bbagen.2024.130685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/03/2024]
Abstract
Plants are exposed to a myriad of stresses, stemming from abiotic and biotic sources, significantly threatening agricultural productivity. The low crop yield, coupled with the global burden of population has resulted in the scarcity of quality food, exacerbating socio-economic issues like poverty, hunger, and malnutrition. Conventional breeding methods for the generation of stress-tolerant plants are time-consuming, limit genetic diversity, and are not sustainable for the consistent production of high-yielding crops. In recent years, the use of high-throughput, genome editing (GE) technique has revolutionized the crop-improvement paradigm, ushering greater prospects for agricultural progress. Among these tools, the Clustered regularly interspaced short palindromic repeat (CRISPR), and its associated nuclease protein Cas9, have appeared as a ground-breaking technology, allowing precise knockout (KO), upregulation, and downregulation of target gene expression. Apart from its high efficacy and speed, this programmable nuclease offers exceptional specificity with minimal off-target effects. Here in, we aim to review the latest findings on the application of the CRISPR/Cas9 genome editing tool for generating resilience in plants against environmental stresses.
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Affiliation(s)
- Sanjib Patra
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Debdatta Chatterjee
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Shrabani Basak
- Department of Biological sciences, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata 700091, West Bengal, India
| | - Susmi Sen
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India
| | - Arunava Mandal
- Department of Genetics, University of Calcutta, 35, Ballygunge circular road, Kolkata 700019, West Bengal, India.
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Razzaq MK, Babur MN, Awan MJA, Raza G, Mobeen M, Aslam A, Siddique KHM. Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential. Funct Integr Genomics 2024; 24:153. [PMID: 39223394 DOI: 10.1007/s10142-024-01435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.
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Affiliation(s)
| | | | - Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences Jhang Road, Faisalabad, Pakistan
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS) PK, Faisalabad, Pakistan
| | - Mehwish Mobeen
- Institute of Pure and Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan, Pakistan
| | - Ali Aslam
- Faculty of Agriculture and Veterinary Sciences, Superior University, Lahore, Pakistan
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
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Zhang J, Wang J, Zhu C, Singh RP, Chen W. Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:429. [PMID: 38337962 PMCID: PMC10856887 DOI: 10.3390/plants13030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
- Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, China
| | - Jingqi Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
| | - Cancan Zhu
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
| | - Raghvendra Pratap Singh
- Department of Research and Development, Biotechnology, Uttaranchal University, Dehradun 248007, India;
| | - Wenfeng Chen
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
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Nawaz M, Sun J, Shabbir S, Khattak WA, Ren G, Nie X, Bo Y, Javed Q, Du D, Sonne C. A review of plants strategies to resist biotic and abiotic environmental stressors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165832. [PMID: 37524179 DOI: 10.1016/j.scitotenv.2023.165832] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Plants exposed to a variety of abiotic and biotic stressors including environmental pollution and global warming pose significant threats to biodiversity and ecosystem services. Despite substantial literature documenting how plants adapt to distinct stressors, there still is a lack of knowledge regarding responses to multiple stressors and how these affects growth and development. Exposure of plants to concurrent biotic and abiotic stressors such as cadmium and drought, leads to pronounced inhibition in above ground biomass, imbalance in oxidative homeostasis, nutrient assimilation and stunted root growth, elucidating the synergistic interactions of multiple stressors culminating in adverse physiological outcomes. Impact of elevated heavy metal and water deficit exposure extends beyond growth and development, influencing the biodiversity of the microenvironment including the rhizosphere nutrient profile and microbiome. These findings have significant implications for plant-stress interactions and ecosystem functioning that prompt immediate action in order to eliminate effect of pollution and address global environmental issues to promote sustainable tolerance for multiple stress combinations in plants. Here, we review plant tolerance against stress combinations, highlighting the need for interdisciplinary approaches and advanced technologies, such as omics and molecular tools, to achieve a comprehensive understanding of underlying stress tolerance mechanisms. To accelerate progress towards developing stress-tolerance in plants against multiple environmental stressors, future research in plant stress tolerance should adopt a collaborative approach, involving researchers from multiple disciplines with diverse expertise and resources.
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Affiliation(s)
- Mohsin Nawaz
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianfan Sun
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Samina Shabbir
- Department of Chemistry, The Women University Multan, Pakistan
| | - Wajid Ali Khattak
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Guangqian Ren
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yanwen Bo
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Qaiser Javed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Christian Sonne
- Aarhus University, Faculty of Technological Sciences, Department of Ecoscience, Frederiksborgvej 399, 358, DK-4000 Roskilde, Denmark; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
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Bouzroud S, Henkrar F, Fahr M, Smouni A. Salt stress responses and alleviation strategies in legumes: a review of the current knowledge. 3 Biotech 2023; 13:287. [PMID: 37520340 PMCID: PMC10382465 DOI: 10.1007/s13205-023-03643-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/21/2023] [Indexed: 08/01/2023] Open
Abstract
Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes' expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes' response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant's priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.
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Affiliation(s)
- Sarah Bouzroud
- Equipe de Microbiologie et Biologie Moléculaire, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
| | - Fatima Henkrar
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Mouna Fahr
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
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Razzaq MK, Hina A, Abbasi A, Karikari B, Ashraf HJ, Mohiuddin M, Maqsood S, Maqsood A, Haq IU, Xing G, Raza G, Bhat JA. Molecular and genetic insights into secondary metabolic regulation underlying insect-pest resistance in legumes. Funct Integr Genomics 2023; 23:217. [PMID: 37392308 DOI: 10.1007/s10142-023-01141-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/03/2023]
Abstract
Insect pests pose a major threat to agricultural production, resulting in significant economic losses for countries. A high infestation of insects in any given area can severely reduce crop yield and quality. This review examines the existing resources for managing insect pests and highlights alternative eco-friendly techniques to enhance insect pest resistance in legumes. Recently, the application of plant secondary metabolites has gained popularity in controlling insect attacks. Plant secondary metabolites encompass a wide range of compounds such as alkaloids, flavonoids, and terpenoids, which are often synthesized through intricate biosynthetic pathways. Classical methods of metabolic engineering involve manipulating key enzymes and regulatory genes to enhance or redirect the production of secondary metabolites in plants. Additionally, the role of genetic approaches, such as quantitative trait loci mapping, genome-wide association (GWAS) mapping, and metabolome-based GWAS in insect pest management is discussed, also, the role of precision breeding, such as genome editing technologies and RNA interference for identifying pest resistance and manipulating the genome to develop insect-resistant cultivars are explored, highlighting the positive contribution of plant secondary metabolites engineering-based resistance against insect pests. It is suggested that by understanding the genes responsible for beneficial metabolite compositions, future research might hold immense potential to shed more light on the molecular regulation of secondary metabolite biosynthesis, leading to advancements in insect-resistant traits in crop plants. In the future, the utilization of metabolic engineering and biotechnological methods may serve as an alternative means of producing biologically active, economically valuable, and medically significant compounds found in plant secondary metabolites, thereby addressing the challenge of limited availability.
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Affiliation(s)
- Muhammad Khuram Razzaq
- Soybean Research Institute & MARA National Centre for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Aiman Hina
- Ministry of Agriculture (MOA) National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Murree, 47150, Pakistan
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Hafiza Javaria Ashraf
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Mohiuddin
- Environmental Management Consultants (EMC) Private Limited, Islamabad, 44000, Pakistan
| | - Sumaira Maqsood
- Department of Environmental Sciences, Kohsar University Murree, Murree, 47150, Pakistan
| | - Aqsa Maqsood
- Department of Zoology, University of Central Punjab, Bahawalpur, 63100, Pakistan
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Guangnan Xing
- Soybean Research Institute & MARA National Centre for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering Faisalabad, Faisalabad, Pakistan
| | - Javaid Akhter Bhat
- International Genome Center, Jiangsu University, Zhenjiang, 212013, 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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Razzaq MK, Rani R, Xing G, Xu Y, Raza G, Aleem M, Iqbal S, Arif M, Mukhtar Z, Nguyen HT, Varshney RK, Siddique KHM, Gai J. Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean ( Glycine max) Growth and Development. Genes (Basel) 2023; 14:1254. [PMID: 37372434 DOI: 10.3390/genes14061254] [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: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I-XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.
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Affiliation(s)
- Muhammad Khuram Razzaq
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Reena Rani
- National Institute for Biotechnology and Genetic Engineering, Faisalabad 38000, Pakistan
| | - Guangnan Xing
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufei Xu
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, Faisalabad 38000, Pakistan
| | - Muqadas Aleem
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan
| | - Shahid Iqbal
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad 38000, Pakistan
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering, Faisalabad 38000, Pakistan
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Junyi Gai
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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9
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Chaudhry A, Hassan AU, Khan SH, Abbasi A, Hina A, Khan MT, Abdelsalam NR. The changing landscape of agriculture: role of precision breeding in developing smart crops. Funct Integr Genomics 2023; 23:167. [PMID: 37204621 DOI: 10.1007/s10142-023-01093-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Food plants play a crucial role in human survival, providing them essential nutrients. However, traditional breeding methods have not been able to keep up with the demands of the growing population. The improvement of food plants aims to increase yield, quality, and resistance to biotic and abiotic stresses. With CRISPR/Cas9, researchers can identify and edit key genes conferring desirable qualities in agricultural plants, including increased yield, enhanced product quality attributes, and increased tolerance to biotic and abiotic challenges. These modifications have enabled the creation of "smart crops" that exhibit rapid climatic adaptation, resistance to extreme weather conditions and high yield and quality. The use of CRISPR/Cas9 combined with viral vectors or growth regulators has made it possible to produce more efficient modified plants with certain conventional breeding methods. However, ethical and regulatory aspects of this technology must be carefully considered. Proper regulation and application of genome editing technology can bring immense benefits to agriculture and food security. This article provides an overview of genetically modified genes and conventional as well as emerging tools, including CRISPR/Cas9, that have been utilized to enhance the quality of plants/fruits and their products. The review also discusses the challenges and prospects associated with these techniques.
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Affiliation(s)
- Amna Chaudhry
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Ahtsham Ul Hassan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, 38040, Pakistan
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, 47150, Pakistan.
| | - Aiman Hina
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Muhammad Tajammal Khan
- Institute of Botany, University of the Punjab, Lahore, 54590, Pakistan
- Division of Science and Technology, Department of Botany, University of Education, Lahore, Pakistan
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
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10
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Jain D, Jones L, Roy S. Gene editing to improve legume-rhizobia symbiosis in a changing climate. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102324. [PMID: 36535148 DOI: 10.1016/j.pbi.2022.102324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
In the last three years, several gene editing techniques have been developed for both model and crop legumes. CRISPR-Cas9-based tools, in particular, are outpacing other comparable gene editing technologies used in legume hosts and their microbial symbionts to understand the molecular basis of symbiotic nitrogen-fixation. Gene editing has helped identify new gene functions, validate genetic screens, resolve gene redundancy, examine the role of tandemly duplicated genes, and investigate symbiotic signaling networks in non-model plants. In this review, we discuss the advances made in understanding the legume-rhizobia symbiosis through the use of gene editing and highlight studies conducted under varying environmental conditions. We reason that future climate-hardy legumes must be able to better integrate environmental signals with nitrogen fixation by fine-tuning long distance signaling, continuing to select efficient rhizobial partners, and adjusting their molecular circuitry to function optimally under variable light and nutrient availability and rising atmospheric carbon dioxide.
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Affiliation(s)
- Divya Jain
- College of Agriculture, Tennessee State University, Nashville, TN 37209, USA
| | - Lauren Jones
- Noble Research Institute, LLC, Ardmore, OK 73401, USA
| | - Sonali Roy
- College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
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11
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CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:cells11233928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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12
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. Life (Basel) 2022; 12:1846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- 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
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
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13
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Abdul Aziz M, Brini F, Rouached H, Masmoudi K. Genetically engineered crops for sustainably enhanced food production systems. FRONTIERS IN PLANT SCIENCE 2022; 13:1027828. [PMID: 36426158 PMCID: PMC9680014 DOI: 10.3389/fpls.2022.1027828] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hatem Rouached
- Michigan State University, Plant and Soil Science Building, East Lansing, MI, United States
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
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14
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Koul B, Sharma K, Sehgal V, Yadav D, Mishra M, Bharadwaj C. Chickpea ( Cicer arietinum L.) Biology and Biotechnology: From Domestication to Biofortification and Biopharming. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212926. [PMID: 36365379 PMCID: PMC9654780 DOI: 10.3390/plants11212926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 05/13/2023]
Abstract
Chickpea (Cicer arietinum L.), the world's second most consumed legume crop, is cultivated in more than 50 countries around the world. It is a boon for diabetics and is an excellent source of important nutrients such as vitamins A, C, E, K, B1-B3, B5, B6, B9 and minerals (Fe, Zn, Mg and Ca) which all have beneficial effects on human health. By 2050, the world population can cross 9 billion, and in order to feed the teaming millions, chickpea production should also be increased, as it is a healthy alternative to wheat flour and a boon for diabetics. Moreover, it is an important legume that is crucial for food, nutrition, and health security and the livelihood of the small-scale farmers with poor resources, in developing countries. Although marvelous improvement has been made in the development of biotic and abiotic stress-resistant varieties, still there are many lacunae, and to fulfill that, the incorporation of genomic technologies in chickpea breeding (genomics-assisted breeding, high-throughput and precise-phenotyping and implementation of novel breeding strategies) will facilitate the researchers in developing high yielding, climate resilient, water use efficient, salt-tolerant, insect/pathogen resistant varieties, acceptable to farmers, consumers, and industries. This review focuses on the origin and distribution, nutritional profile, genomic studies, and recent updates on crop improvement strategies for combating abiotic and biotic stresses in chickpea.
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Affiliation(s)
- Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Komal Sharma
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Vrinda Sehgal
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Meerambika Mishra
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi 110012, India
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15
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Jianing G, Yuhong G, Yijun G, Rasheed A, Qian Z, Zhiming X, Mahmood A, Shuheng Z, Zhuo Z, Zhuo Z, Xiaoxue W, Jian W. Improvement of heat stress tolerance in soybean ( Glycine max L), by using conventional and molecular tools. FRONTIERS IN PLANT SCIENCE 2022; 13:993189. [PMID: 36226280 PMCID: PMC9549248 DOI: 10.3389/fpls.2022.993189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
The soybean is a significant legume crop, providing several vital dietary components. Extreme heat stress negatively affects soybean yield and quality, especially at the germination stage. Continuous change in climatic conditions is threatening the global food supply and food security. Therefore, it is a critical need of time to develop heat-tolerant soybean genotypes. Different molecular techniques have been developed to improve heat stress tolerance in soybean, but until now complete genetic mechanism of soybean is not fully understood. Various molecular methods, like quantitative trait loci (QTL) mapping, genetic engineering, transcription factors (TFs), transcriptome, and clustered regularly interspaced short palindromic repeats (CRISPR), are employed to incorporate heat tolerance in soybean under the extreme conditions of heat stress. These molecular techniques have significantly improved heat stress tolerance in soybean. Besides this, we can also use specific classical breeding approaches and different hormones to reduce the harmful consequences of heat waves on soybean. In future, integrated use of these molecular tools would bring significant results in developing heat tolerance in soybean. In the current review, we have presented a detailed overview of the improvement of heat tolerance in soybean and highlighted future prospective. Further studies are required to investigate different genetic factors governing the heat stress response in soybean. This information would be helpful for future studies focusing on improving heat tolerance in soybean.
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Affiliation(s)
- Guan Jianing
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Gai Yuhong
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Guan Yijun
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Adnan Rasheed
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Zhao Qian
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Xie Zhiming
- College of Life Sciences, Baicheng Normal University, Baicheng, China
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zhang Shuheng
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhang Zhuo
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhao Zhuo
- College of Life Sciences, Jilin Normal University, Changchun, China
| | - Wang Xiaoxue
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wei Jian
- College of Life Sciences, Changchun Normal University, Changchun, China
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