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Bharti J, Verma R, Gupta I, Chakraborty P, Eashwaran M, Sony SK, Nehra M, Thangraj A, Kaul R, Fathy K, Kaul T. Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design. J Biomol Struct Dyn 2024; 42:6065-6080. [PMID: 37652402 DOI: 10.1080/07391102.2023.2243522] [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: 02/02/2023] [Accepted: 06/21/2023] [Indexed: 09/02/2023]
Abstract
Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the in-silico analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized in-silico validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level via molecular dynamic (MD) simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyotsna Bharti
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Isha Gupta
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puja Chakraborty
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Murugesh Eashwaran
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Mamta Nehra
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Arulprakash Thangraj
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Khaled Fathy
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Tanushri Kaul
- Nutritional Improvement of Crops Group, Plant Biology & Biotechnology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Nadeem S, Riaz Ahmed S, Luqman T, Tan DKY, Maryum Z, Akhtar KP, Muhy Ud Din Khan S, Tariq MS, Muhammad N, Khan MKR, Liu Y. A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus. Front Genet 2024; 15:1306469. [PMID: 38440193 PMCID: PMC10909863 DOI: 10.3389/fgene.2024.1306469] [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: 10/03/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.
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Affiliation(s)
- Sahar Nadeem
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Pakistan Agriculture Research Council (PARC), Horticulture Research Institute Khuzdar Baghbana, Khuzdar, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Zahra Maryum
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Nazar Muhammad
- Agriculture and Cooperative Department, Quetta, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Kumam Y, Trick HN, Vara Prasad P, Jugulam M. Transformative Approaches for Sustainable Weed Management: The Power of Gene Drive and CRISPR-Cas9. Genes (Basel) 2023; 14:2176. [PMID: 38136999 PMCID: PMC10742955 DOI: 10.3390/genes14122176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Weeds can negatively impact crop yields and the ecosystem's health. While many weed management strategies have been developed and deployed, there is a greater need for the development of sustainable methods for employing integrated weed management. Gene drive systems can be used as one of the approaches to suppress the aggressive growth and reproductive behavior of weeds, although their efficacy is yet to be tested. Their popularity in insect pest management has increased, however, with the advent of CRISPR-Cas9 technology, which provides specificity and precision in editing the target gene. This review focuses on the different types of gene drive systems, including the use of CRISPR-Cas9-based systems and their success stories in pest management, while also exploring their possible applications in weed species. Factors that govern the success of a gene drive system in weeds, including the mode of reproduction, the availability of weed genome databases, and well-established transformation protocols are also discussed. Importantly, the risks associated with the release of weed populations with gene drive-bearing alleles into wild populations are also examined, along with the importance of addressing ecological consequences and ethical concerns.
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Affiliation(s)
- Yaiphabi Kumam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA;
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
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Manchanda P, Kaur H, Khan F, Sidhu GS, Hunjan MS, Chhuneja P, Bains NS. Agroinfiltration-based transient genome editing for targeting phytoene desaturase gene in kinnow mandarin (C. reticulata Blanco). Mol Biotechnol 2023:10.1007/s12033-023-00980-z. [PMID: 38041775 DOI: 10.1007/s12033-023-00980-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023]
Abstract
Citrus reticulata Blanco also known as kinnow mandarin is a widely grown horticultural crop in Punjab. CRISPR/Cas9 technology is being widely used for generation of varieties with increased resilience towards abiotic and biotic stresses as well as improved horticultural traits. Xanthomonas citri subsp. citri (Xcc)-mediated Agroinfiltration offers a fast and transgene-free method for the delivery of CRISPR/Cas9 constructs for systemic introduction into plants for functional genomics and expression studies. The technology is currently unexplored in kinnow mandarin. This study is aimed at establishing an efficient method of Cas9 delivery for transient knockout of PDS (phytoene desaturase) gene in kinnow mandarin. The construct pKO-119-PDS N-Cas9/sgRNA:PDS1 carrying sgRNA and Cas9 enzyme was delivered into the dorsal surface of young leaves of kinnow mandarin. The leaves showed albino patches at the point of injection within 60 h. Two surfactants (Triton-X and Silwet™) were used to ease the Agroinfiltration process which resulted in variation in the expression of vector. The Sanger's analysis of the treated plants showed a substitution within the sgRNA region which resulted in change in amino acid from proline to serine. The protocol provides a feasible and an efficient method for genome editing in C. reticulata which could be helpful in future studies aimed at genome editing as well as genetic transformation.
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Affiliation(s)
- Pooja Manchanda
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Harleen Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Faishal Khan
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar S Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Mandeep S Hunjan
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Navtej S Bains
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
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Joshi A, Yang SY, Song HG, Min J, Lee JH. Genetic Databases and Gene Editing Tools for Enhancing Crop Resistance against Abiotic Stress. BIOLOGY 2023; 12:1400. [PMID: 37997999 PMCID: PMC10669554 DOI: 10.3390/biology12111400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
Abiotic stresses extensively reduce agricultural crop production globally. Traditional breeding technology has been the fundamental approach used to cope with abiotic stresses. The development of gene editing technology for modifying genes responsible for the stresses and the related genetic networks has established the foundation for sustainable agriculture against environmental stress. Integrated approaches based on functional genomics and transcriptomics are now expanding the opportunities to elucidate the molecular mechanisms underlying abiotic stress responses. This review summarizes some of the features and weblinks of plant genome databases related to abiotic stress genes utilized for improving crops. The gene-editing tool based on clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized stress tolerance research due to its simplicity, versatility, adaptability, flexibility, and broader applications. However, off-target and low cleavage efficiency hinder the successful application of CRISPR/Cas systems. Computational tools have been developed for designing highly competent gRNA with better cleavage efficiency. This powerful genome editing tool offers tremendous crop improvement opportunities, overcoming conventional breeding techniques' shortcomings. Furthermore, we also discuss the mechanistic insights of the CRISPR/Cas9-based genome editing technology. This review focused on the current advances in understanding plant species' abiotic stress response mechanism and applying the CRISPR/Cas system genome editing technology to develop crop resilience against drought, salinity, temperature, heavy metals, and herbicides.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea;
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
| | - Hyung-Geun Song
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
| | - Jiho Min
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea;
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
- Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Zhang C, Zhong X, Li S, Yan L, Li J, He Y, Lin Y, Zhang Y, Xia L. Artificial evolution of OsEPSPS through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2194-2203. [PMID: 37402157 DOI: 10.1111/jipb.13543] [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: 03/27/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023]
Abstract
Exploiting novel endogenous glyphosate-tolerant alleles is highly desirable and has promising potential for weed control in rice breeding. Here, through fusions of different effective cytosine and adenine deaminases with nCas9-NG, we engineered an effective surrogate two-component composite base editing system, STCBE-2, with improved C-to-T and A-to-G base editing efficiency and expanded the editing window. Furthermore, we targeted a rice endogenous OsEPSPS gene for artificial evolution through STCBE-2-mediated near-saturated mutagenesis. After hygromycin and glyphosate selection, we identified a novel OsEPSPS allele with an Asp-213-Asn (D213N) mutation (OsEPSPS-D213N) in the predicted glyphosate-binding domain, which conferred rice plants reliable glyphosate tolerance and had not been reported or applied in rice breeding. Collectively, we developed a novel dual base editor which will be valuable for artificial evolution of important genes in crops. And the novel glyphosate-tolerant rice germplasm generated in this study will benefit weeds management in rice paddy fields.
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Affiliation(s)
- Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xue Zhong
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CAAS/Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Sanya, 572024, China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CAAS/Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Sanya, 572024, China
- Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agricultural and Rural Affairs, Sanya, 572024, China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CAAS/Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Sanya, 572024, China
- Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agricultural and Rural Affairs, Sanya, 572024, China
| | - Yubing He
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CAAS/Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Sanya, 572024, China
- Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agricultural and Rural Affairs, Sanya, 572024, China
| | - Yong Lin
- Beijing Dabeinong Technology Group Co., Ltd, Beijing, 10080, China
| | - Yangjun Zhang
- Beijing Dabeinong Technology Group Co., Ltd, Beijing, 10080, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CAAS/Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Sanya, 572024, China
- Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agricultural and Rural Affairs, Sanya, 572024, China
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