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Long L, Xu FC, Yuan M, Shang SZ, Song HG, Zhao JR, Hu GY, Zhang ZN, Zhao XT, Ma JY, Hussain A, Wang P, Cai YF, Jin SX, Gao W. GhHAM regulates GoPGF-dependent gland development and contributes to broad-spectrum pest resistance in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:879-894. [PMID: 38923085 DOI: 10.1111/tpj.16803] [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: 12/09/2023] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 06/28/2024]
Abstract
Cotton is a globally cultivated crop, producing 87% of the natural fiber used in the global textile industry. The pigment glands, unique to cotton and its relatives, serve as a defense structure against pests and pathogens. However, the molecular mechanism underlying gland formation and the specific role of pigment glands in cotton's pest defense are still not well understood. In this study, we cloned a gland-related transcription factor GhHAM and generated the GhHAM knockout mutant using CRISPR/Cas9. Phenotypic observations, transcriptome analysis, and promoter-binding experiments revealed that GhHAM binds to the promoter of GoPGF, regulating pigment gland formation in cotton's multiple organs via the GoPGF-GhJUB1 module. The knockout of GhHAM significantly reduced gossypol production and increased cotton's susceptibility to pests in the field. Feeding assays demonstrated that more than 80% of the cotton bollworm larvae preferred ghham over the wild type. Furthermore, the ghham mutants displayed shorter cell length and decreased gibberellins (GA) production in the stem. Exogenous application of GA3 restored stem cell elongation but not gland formation, thereby indicating that GhHAM controls gland morphogenesis independently of GA. Our study sheds light on the functional differentiation of HAM proteins among plant species, highlights the significant role of pigment glands in influencing pest feeding preference, and provides a theoretical basis for breeding pest-resistant cotton varieties to address the challenges posed by frequent outbreaks of pests.
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Affiliation(s)
- Lu Long
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Fu-Chun Xu
- Changzhi Medical College, Changzhi, Shanxi, 046000, P.R. China
| | - Man Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Shen-Zhai Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Hao-Ge Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Jing-Ruo Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Gai-Yuan Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
- Sanya Institute of Henan University, Sanya, Hainan, 572024, P.R. China
| | - Zhen-Nan Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Xiao-Tong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Jia-Yi Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Amjad Hussain
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Ping Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Ying-Fan Cai
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
| | - Shuang-Xia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Wei Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Science, Henan University, Kaifeng, Henan, 475004, P.R. China
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Ijaz U, Zhao C, Shabala S, Zhou M. Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context. BIOLOGY 2024; 13:421. [PMID: 38927301 PMCID: PMC11200688 DOI: 10.3390/biology13060421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia;
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
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3
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Yi F, Li Y, Song A, Shi X, Hu S, Wu S, Shao L, Chu Z, Xu K, Li L, Tran LP, Li W, Cai Y. Positive roles of the Ca 2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance. MOLECULAR PLANT PATHOLOGY 2024; 25:e13483. [PMID: 38829344 PMCID: PMC11146148 DOI: 10.1111/mpp.13483] [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: 03/07/2024] [Revised: 04/18/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
As a universal second messenger, cytosolic calcium (Ca2+) functions in multifaceted intracellular processes, including growth, development and responses to biotic/abiotic stresses in plant. The plant-specific Ca2+ sensors, calmodulin and calmodulin-like (CML) proteins, function as members of the second-messenger system to transfer Ca2+ signal into downstream responses. However, the functions of CMLs in the responses of cotton (Gossypium spp.) after Verticillium dahliae infection, which causes the serious vascular disease Verticillium wilt, remain elusive. Here, we discovered that the expression level of GbCML45 was promoted after V. dahliae infection in roots of cotton, suggesting its potential role in Verticillium wilt resistance. We found that knockdown of GbCML45 in cotton plants decreased resistance while overexpression of GbCML45 in Arabidopsis thaliana plants enhanced resistance to V. dahliae infection. Furthermore, there was physiological interaction between GbCML45 and its close homologue GbCML50 by using yeast two-hybrid and bimolecular fluorescence assays, and both proteins enhanced cotton resistance to V. dahliae infection in a Ca2+-dependent way in a knockdown study. Detailed investigations indicated that several defence-related pathways, including salicylic acid, ethylene, reactive oxygen species and nitric oxide signalling pathways, as well as accumulations of lignin and callose, are responsible for GbCML45- and GbCML50-modulated V. dahliae resistance in cotton. These results collectively indicated that GbCML45 and GbCML50 act as positive regulators to improve cotton Verticillium wilt resistance, providing potential targets for exploitation of improved Verticillium wilt-tolerant cotton cultivars by genetic engineering and molecular breeding.
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Affiliation(s)
- Feifei Yi
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Yuzhe Li
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Aosong Song
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Xinying Shi
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Shanci Hu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Shuang Wu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Lili Shao
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Zongyan Chu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Kun Xu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Liangliang Li
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Lam‐Son Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress ResistanceTexas Tech UniversityLubbockTexasUSA
| | - Weiqiang Li
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Yingfan Cai
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
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Gong J, Sun S, Zhu QH, Qin J, Yang Y, Zheng Z, Cheng S, Sun J. Gh4CL20/20A involved in flavonoid biosynthesis is essential for male fertility in cotton (Gossypium hirsutum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108484. [PMID: 38452452 DOI: 10.1016/j.plaphy.2024.108484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Flavonoids have been shown to play an essential role in plant growth and fertility. 4-Coumarate CoA ligase (4CL) is one of the indispensable enzymes involved in the biosynthesis of flavonoids. However, the role of 4CL and flavonoids in impact on cotton fertility is still unknown. In this study, on the basis of identification of an additional Gh4CL gene, Gh4CL20A, by using an updated G. hirsutum genome, we found that Gh4CL20A and its homologous Gh4CL20 were preferentially expressed in petals and stamens. The petals of the loss-of-function Gh4CL20/Gh4CL20A mutant generated by CRISPR/Cas9 gene editing remained white until wilting. Notably, the mutant showed indehiscent anthers, reduced number of pollen grains and pollen viability, leading to male sterility. Histological analysis revealed that abnormal degradation of anther tapetum at the tetrad stage and abnormal pollen grain development at the mature stage caused male sterility of the gene editing mutant. Analysis of the anther transcriptome identified a total of 10574 and 11962 genes up- and down-regulated in the mutant, respectively, compared to the wild-type. GO, KEGG, and WGCNA analyses linked the abnormality of the mutant anthers to the defective flavonoid biosynthetic pathway, leading to decreased activity of 4CL and chalcone isomerase (CHI) and reduced accumulation of flavonoids in the mutant. These results imply a role of Gh4CL20/Gh4CL20A in assuring proper development of cotton anthers by regulating flavonoid metabolism. This study elucidates a molecular mechanism underlying cotton anther development and provides candidate genes for creating cotton male sterile germplasm that has the potential to be used in production of hybrid seeds.
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Affiliation(s)
- Junming Gong
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China.
| | - Shichao Sun
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China.
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australia.
| | - Jianghong Qin
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, China.
| | - Yonglin Yang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, China.
| | - Zhihong Zheng
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, China.
| | - Shuaishuai Cheng
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China.
| | - Jie Sun
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China.
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5
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Guo WF, Guo DD, Li F, Shang SZ, Li TW, Tang YC, Jiang M, Xu FC, Gao W. Efficient genome editing in cotton using the virus-mediated CRISPR/Cas9 and grafting system. PLANT CELL REPORTS 2023; 42:1833-1836. [PMID: 37642675 DOI: 10.1007/s00299-023-03061-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
KEY MESSAGE The extensive application of CRISPR in cotton was limited due to the labor-intensive transformation process. Thus, we here established a convenient method of CRISPR in cotton by CLCrV-mediated sgRNA delivery.
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Affiliation(s)
- Wei-Feng Guo
- Agricultural College, Tarim University, Alaer, Xinjiang, People's Republic of China
| | - Dan-Dan Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Fen Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Shen-Zhai Shang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Ting-Wan Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Ying-Chao Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Man Jiang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China
| | - Fu-Chun Xu
- Changzhi Medical College, Changzhi, Shanxi, People's Republic of China
| | - Wei Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan, 475004, People's Republic of China.
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6
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Sabnam N, Hussain A, Saha P. The secret password: Cell death-inducing proteins in filamentous phytopathogens - As versatile tools to develop disease-resistant crops. Microb Pathog 2023; 183:106276. [PMID: 37541554 DOI: 10.1016/j.micpath.2023.106276] [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: 05/05/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Cell death-inducing proteins (CDIPs) are some of the secreted effector proteins manifested by filamentous oomycetes and fungal pathogens to invade the plant tissue and facilitate infection. Along with their involvement in different developmental processes and virulence, CDIPs play a crucial role in plant-pathogen interactions. As the name implies, CDIPs cause necrosis and trigger localised cell death in the infected host tissues by the accumulation of higher concentrations of hydrogen peroxide (H2O2), oxidative burst, accumulation of nitric oxide (NO), and electrolyte leakage. They also stimulate the biosynthesis of defense-related phytohormones such as salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET), as well as the expression of pathogenesis-related (PR) genes that are important in disease resistance. Altogether, the interactions result in the hypersensitive response (HR) in the host plant, which might confer systemic acquired resistance (SAR) in some cases against a vast array of related and unrelated pathogens. The CDIPs, due to their capability of inducing host resistance, are thus unique among the array of proteins secreted by filamentous plant pathogens. More interestingly, a few transgenic plant lines have also been developed expressing the CDIPs with added resistance. Thus, CDIPs have opened an interesting hot area of research. The present study critically reviews the current knowledge of major types of CDIPs identified across filamentous phytopathogens and their modes of action in the last couple of years. This review also highlights the recent breakthrough technologies in studying plant-pathogen interactions as well as crop improvement by enhancing disease resistance through CDIPs.
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Affiliation(s)
- Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India.
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Pallabi Saha
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, United States; Department of Biotechnology, National Institute of Technology, Durgapur, India
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8
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Shakoor S, Rao AQ, Ajmal S, Yasmeen A, Khan MAU, Sadaqat S, Ashraf NM, Wolter F, Pacher M, Husnain T. Multiplex Cas9-based excision of CLCuV betasatellite and DNA-A revealed reduction of viral load with asymptomatic cotton plants. PLANTA 2023; 258:79. [PMID: 37698688 DOI: 10.1007/s00425-023-04233-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/27/2023] [Indexed: 09/13/2023]
Abstract
MAIN CONCLUSION Multiplexed Cas9-based genome editing of cotton resulted in reduction of viral load with asymptomatic cotton plants. In depth imaging of proteomic dynamics of resulting CLCuV betasatellite and DNA-A protein was also performed. The notorious cotton leaf curl virus (CLCuV), which is transmitted by the sap-sucking insect whitefly, continuously damages cotton crops. Although the application of various toxins and RNAi has shown some promise, sustained control has not been achieved. Consequently, CRISPR_Cas9 was applied by designing multiplex targets against DNA-A (AC2 and AC3) and betasatellite (βC1) of CLCuV using CRISPR direct and ligating into the destination vector of the plant using gateway ligation method. The successful ligation of targets into the destination vector was confirmed by the amplification of 1049 bp using a primer created from the promoter and target, while restriction digestion using the AflII and Asc1 enzymes determined how compact the plasmid developed and the nucleotide specificity of the plasmid was achieved through Sanger sequencing. PCR confirmed the successful introduction of plasmid into CKC-1 cotton variety. Through Sanger sequencing and correlation with the mRNA expression of DNA-A and betasatellite in genome-edited cotton plants subjected to agroinfiltration of CLCuV infectious clone, the effectiveness of knockout was established. The genome-edited cotton plants demonstrated edited efficacy of 72% for AC2 and AC3 and 90% for the (βC1) through amplicon sequencing, Molecular dynamics (MD) simulations were used to further validate the results. Higher RMSD values for the edited βC1 and AC3 proteins indicated functional loss caused by denaturation. Thus, CRISPR_Cas9 constructs can be rationally designed using high-throughput MD simulation technique. The confidence in using this technology to control plant virus and its vector was determined by the knockout efficiency and the virus inoculation assay.
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Affiliation(s)
- Sana Shakoor
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan
| | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan.
| | - Sara Ajmal
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan
| | - Aneela Yasmeen
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan
| | | | - Sahar Sadaqat
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Felix Wolter
- Pacific Biosciences, Bonn, Nordrhein-Westfalen, Deutschland
| | - Michael Pacher
- CureVac Manufacturing GmbH, Tübingen, Baden-Württemberg, Deutschland
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, 53700, Pakistan
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9
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Mainkar P, Manape TK, Satheesh V, Anandhan S. CRISPR/Cas9-mediated editing of PHYTOENE DESATURASE gene in onion ( Allium cepa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226911. [PMID: 37701798 PMCID: PMC10494252 DOI: 10.3389/fpls.2023.1226911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/28/2023] [Indexed: 09/14/2023]
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) is a precise genome editing tool used to introduce genetic modifications in a wide range of crop species. Thus far, there is no report of CRISPR/Cas9-mediated genome editing in onions (Allium cepa L.). Methods In the present study, we targeted two exons of the gene coding for Phytoene desaturase (AcPDS) in onion cv. Bhima Super. The sgRNA-carrying constructs were co-cultivated with 8-week-old embryogenic calli using an Agrobacterium-mediated transformation protocol and incubated on the media without hygromycin B selection. Results and discussion Out of the total 617 co-cultivated calli, 21 (3.4%) regenerated shoots exhibited three distinct phenotypes: albino, chimeric, and pale green; in comparison to the wild-type non-transformed regenerated shoots. Total chlorophyll content was drastically reduced in albino shoots and significantly decreased in chimeric shoots. Out of the six Cas9 gene PCR-confirmed regenerated shoots, two exhibited the albino phenotype due to insertions/deletions (InDels) and substitution-based mutations in and around the AcPDS target sites. Deep amplicon sequencing revealed a significantly variable InDel frequency between two sgRNAs, ranging from 1.2% to 63.4%, along with a 53.4% substitution frequency. The mutation of the AcPDS gene generated a visually detectable albino phenotype, thus confirming the successful editing of the AcPDS gene. This is the first time a CRISPR/Cas9-mediated genome editing protocol has been successfully established in onion, with the AcPDS gene serving as an example. This study will provide the necessary momentum for researchers to further basic and applied research on onions.
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Affiliation(s)
- Pawan Mainkar
- ICAR-Directorate of Onion and Garlic Research, Pune, Maharashtra, India
| | | | - Viswanathan Satheesh
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, United States
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Ali A, Zafar MM, Farooq Z, Ahmed SR, Ijaz A, Anwar Z, Abbas H, Tariq MS, Tariq H, Mustafa M, Bajwa MH, Shaukat F, Razzaq A, Maozhi R. Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnol J 2023; 18:e2200642. [PMID: 37166088 DOI: 10.1002/biot.202200642] [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: 12/25/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.
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Affiliation(s)
- Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | | | - Zunaira Farooq
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Huma Abbas
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Hala Tariq
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mahwish Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Fiza Shaukat
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdul Razzaq
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ren Maozhi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of, Urban Agriculture, Chinese Academy of Agriculture Science, Chengdu, China
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Anuradha, Kumari M, Zinta G, Chauhan R, Kumar A, Singh S, Singh S. Genetic resources and breeding approaches for improvement of amaranth ( Amaranthus spp.) and quinoa ( Chenopodium quinoa). Front Nutr 2023; 10:1129723. [PMID: 37554703 PMCID: PMC10405290 DOI: 10.3389/fnut.2023.1129723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.
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Affiliation(s)
- Anuradha
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Manisha Kumari
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Gaurav Zinta
- Division of Biotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ramesh Chauhan
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ashok Kumar
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Sanatsujat Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Satbeer Singh
- Division of Agrotechnology, Council of Scientific and Industrial Research–Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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Ingvardsen CR, Brinch-Pedersen H. Challenges and potentials of new breeding techniques in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1154332. [PMID: 37360738 PMCID: PMC10285108 DOI: 10.3389/fpls.2023.1154332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
Cannabis sativa L. is an ancient crop used for fiber and seed production and not least for its content of cannabinoids used for medicine and as an intoxicant drug. Due to the psychedelic effect of one of the compounds, tetrahydrocannabinol (THC), many countries had regulations or bands on Cannabis growing, also as fiber or seed crop. Recently, as many of these regulations are getting less tight, the interest for the many uses of this crop is increasing. Cannabis is dioecious and highly heterogenic, making traditional breeding costly and time consuming. Further, it might be difficult to introduce new traits without changing the cannabinoid profile. Genome editing using new breeding techniques might solve these problems. The successful use of genome editing requires sequence information on suitable target genes, a genome editing tool to be introduced into plant tissue and the ability to regenerate plants from transformed cells. This review summarizes the current status of Cannabis breeding, uncovers potentials and challenges of Cannabis in an era of new breeding techniques and finally suggests future focus areas that may help to improve our overall understanding of Cannabis and realize the potentials of the plant.
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Yi F, Song A, Cheng K, Liu J, Wang C, Shao L, Wu S, Wang P, Zhu J, Liang Z, Chang Y, Chu Z, Cai C, Zhang X, Wang P, Chen A, Xu J, Burritt DJ, Herrera-Estrella L, Tran LSP, Li W, Cai Y. Strigolactones positively regulate Verticillium wilt resistance in cotton via crosstalk with other hormones. PLANT PHYSIOLOGY 2023; 192:945-966. [PMID: 36718522 PMCID: PMC10231467 DOI: 10.1093/plphys/kiad053] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/01/2023]
Abstract
Verticillium wilt caused by Verticillium dahliae is a serious vascular disease in cotton (Gossypium spp.). V. dahliae induces the expression of the CAROTENOID CLEAVAGE DIOXYGENASE 7 (GauCCD7) gene involved in strigolactone (SL) biosynthesis in Gossypium australe, suggesting a role for SLs in Verticillium wilt resistance. We found that the SL analog rac-GR24 enhanced while the SL biosynthesis inhibitor TIS108 decreased cotton resistance to Verticillium wilt. Knock-down of GbCCD7 and GbCCD8b genes in island cotton (Gossypium barbadense) decreased resistance, whereas overexpression of GbCCD8b in upland cotton (Gossypium hirsutum) increased resistance to Verticillium wilt. Additionally, Arabidopsis (Arabidopsis thaliana) SL mutants defective in CCD7 and CCD8 putative orthologs were susceptible, whereas both Arabidopsis GbCCD7- and GbCCD8b-overexpressing plants were more resistant to Verticillium wilt than wild-type (WT) plants. Transcriptome analyses showed that several genes related to the jasmonic acid (JA)- and abscisic acid (ABA)-signaling pathways, such as MYELOCYTOMATOSIS 2 (GbMYC2) and ABA-INSENSITIVE 5, respectively, were upregulated in the roots of WT cotton plants in responses to rac-GR24 and V. dahliae infection but downregulated in the roots of both GbCCD7- and GbCCD8b-silenced cotton plants. Furthermore, GbMYC2 suppressed the expression of GbCCD7 and GbCCD8b by binding to their promoters, which might regulate the homeostasis of SLs in cotton through a negative feedback loop. We also found that GbCCD7- and GbCCD8b-silenced cotton plants were impaired in V. dahliae-induced reactive oxygen species (ROS) accumulation. Taken together, our results suggest that SLs positively regulate cotton resistance to Verticillium wilt through crosstalk with the JA- and ABA-signaling pathways and by inducing ROS accumulation.
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Affiliation(s)
- Feifei Yi
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Aosong Song
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Kai Cheng
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jinlei Liu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Chenxiao Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Lili Shao
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Shuang Wu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Ping Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jiaxuan Zhu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Zhilin Liang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Ying Chang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Zongyan Chu
- Cotton Institution, Kaifeng Academy of Agriculture and Forestry, Kaifeng 475000, China
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Pei Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Aimin Chen
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China
| | - David J Burritt
- Department of Botany, University of Otago, Dunedin 9054, New Zealand
| | - Luis Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
- Unidad de Genomica Avanzada, Centro de Investigaciony de Estudios Avanzados del Intituto Politecnico Nacional, Irapuato 36821, Mexico
| | - Lam-Son Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Jilin Da’an Agro-ecosystem National Observation Research Station, Changchun 130102, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
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Wang Z, Shea Z, Rosso L, Shang C, Li J, Bewick P, Li Q, Zhao B, Zhang B. Development of new mutant alleles and markers for KTI1 and KTI3 via CRISPR/Cas9-mediated mutagenesis to reduce trypsin inhibitor content and activity in soybean seeds. FRONTIERS IN PLANT SCIENCE 2023; 14:1111680. [PMID: 37223818 PMCID: PMC10200896 DOI: 10.3389/fpls.2023.1111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
The digestibility of soybean meal can be severely impacted by trypsin inhibitor (TI), one of the most abundant anti-nutritional factors present in soybean seeds. TI can restrain the function of trypsin, a critical enzyme that breaks down proteins in the digestive tract. Soybean accessions with low TI content have been identified. However, it is challenging to breed the low TI trait into elite cultivars due to a lack of molecular markers associated with low TI traits. We identified Kunitz trypsin inhibitor 1 (KTI1, Gm01g095000) and KTI3 (Gm08g341500) as two seed-specific TI genes. Mutant kti1 and kti3 alleles carrying small deletions or insertions within the gene open reading frames were created in the soybean cultivar Glycine max cv. Williams 82 (WM82) using the CRISPR/Cas9-mediated genome editing approach. The KTI content and TI activity both remarkably reduced in kti1/3 mutants compared to the WM82 seeds. There was no significant difference in terms of plant growth or maturity days of kti1/3 transgenic and WM82 plants in greenhouse condition. We further identified a T1 line, #5-26, that carried double homozygous kti1/3 mutant alleles, but not the Cas9 transgene. Based on the sequences of kti1/3 mutant alleles in #5-26, we developed markers to co-select for these mutant alleles by using a gel-electrophoresis-free method. The kti1/3 mutant soybean line and associated selection markers will assist in accelerating the introduction of low TI trait into elite soybean cultivars in the future.
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Affiliation(s)
- Zhibo Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Zachary Shea
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Luciana Rosso
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chao Shang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Patrick Bewick
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Qi Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Sony SK, Kaul T, Motelb KFA, Thangaraj A, Bharti J, Kaul R, Verma R, Nehra M. CRISPR/Cas9-mediated homology donor repair base editing confers glyphosate resistance to rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1122926. [PMID: 36959937 PMCID: PMC10027715 DOI: 10.3389/fpls.2023.1122926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Globally, CRISPR-Cas9-based genome editing has ushered in a novel era of crop advancements. Weeds pose serious a threat to rice crop productivity. Among the numerous herbicides, glyphosate [N-(phosphonomethyl)-glycine] has been employed as a post-emergent, broad-spectrum herbicide that represses the shikimate pathway via inhibition of EPSPS (5'-enolpyruvylshikimate-3-phosphate synthase) enzyme in chloroplasts. Here, we describe the development of glyphosate-resistant rice lines by site-specific amino acid substitutions (G172A, T173I, and P177S: GATIPS-mOsEPSPS) and modification of phosphoenolpyruvate-binding site in the native OsEPSPS gene employing fragment knockout and knock-in of homology donor repair (HDR) template harboring desired mutations through CRISPR-Cas9-based genome editing. The indigenously designed two-sgRNA OsEPSPS-NICTK-1_pCRISPR-Cas9 construct harboring rice codon-optimized SpCas9 along with OsEPSPS-HDR template was transformed into rice. Stable homozygous T2 edited rice lines revealed significantly high degree of glyphosate-resistance both in vitro (4 mM/L) and field conditions (6 ml/L; Roundup Ready) in contrast to wild type (WT). Edited T2 rice lines (ER1-6) with enhanced glyphosate resistance revealed lower levels of endogenous shikimate (14.5-fold) in contrast to treated WT but quite similar to WT. ER1-6 lines exhibited increased aromatic amino acid contents (Phe, two-fold; Trp, 2.5-fold; and Tyr, two-fold) than WT. Interestingly, glyphosate-resistant Cas9-free EL1-6 rice lines displayed a significant increment in grain yield (20%-22%) in comparison to WT. Together, results highlighted that the efficacy of GATIPS mutations in OsEPSPS has tremendously contributed in glyphosate resistance (foliar spray of 6 ml/L), enhanced aromatic amino acids, and improved grain yields in rice. These results ensure a novel strategy for weed management without yield penalties, with a higher probability of commercial release.
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Akhtar S, Shahid AA, Shakoor S, Ahmed M, Iftikhar S, Usmaan M, Sadaqat S, Latif A, Iqbal A, Rao AQ. Tissue specific expression of bacterial cellulose synthase (Bcs) genes improves cotton fiber length and strength. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111576. [PMID: 36565935 DOI: 10.1016/j.plantsci.2022.111576] [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: 07/21/2022] [Revised: 11/27/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Fiber growing inside the cotton bolls is a highly demandable product and its quality is key to the success of the textile industry. Despite the various efforts to improve cotton fiber staple length Pakistan has to import millions of bales to sustain its industrial needs. To improve cotton fiber quality Bacterial cellulose synthase (Bcs) genes (acsA, acsB) were expressed in a local cotton variety CEMB-00. In silico studies revealed a number of conserved domains both in the cotton-derived and bacterial cellulose synthases which are essential for the cellulose synthesis. Transformation efficiency of 1.27% was achieved by using Agrobacterium shoot apex cut method of transformation. The quantitative mRNA expression analysis of the Bcs genes in transgenic cotton fiber was found to be many folds higher during secondary cell wall synthesis stage (35 DPA) than the expression during elongation phase (10 DPA). Average fiber length of the transgenic cotton plant lines S-00-07, S-00-11, S-00-16 and S-00-23 was calculated to be 13.02% higher than that of the non-transgenic control plants. Likewise, the average fiber strength was found to be 20.92% higher with an enhanced cellulose content of 22.45%. The mutated indigenous cellulose synthase genes of cotton generated through application of CRISPR/Cas9 resulted in 6.03% and 12.10% decrease in fiber length and strength respectively. Furthermore, mature cotton fibers of transgenic cotton plants were found to have increased number of twists with smooth surface as compared to non-transgenic control when analyzed under scanning electron microscope. XRD analysis of cotton fibers revealed less cellulose crystallinity index in transgenic cotton fibers as compared to control fibers due to deposition of more amorphous cellulose in transgenic fibers as a result of Bcs gene expression. This study paved the way towards unraveling the fact that Bcs genes influence cellulose synthase activity and this enzyme helps in determining the fate of cotton fiber length and strength.
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Affiliation(s)
- Sidra Akhtar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sana Shakoor
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mukhtar Ahmed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; Government Boys College Sokasan Bhimber, Higher Education Department (HED), Azad Jaumm and Kashmir, Pakistan
| | - Sehrish Iftikhar
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usmaan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sahar Sadaqat
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ayesha Latif
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Adnan Iqbal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Zhang K, Liu S, Fu Y, Wang Z, Yang X, Li W, Zhang C, Zhang D, Li J. Establishment of an efficient cotton root protoplast isolation protocol suitable for single-cell RNA sequencing and transient gene expression analysis. PLANT METHODS 2023; 19:5. [PMID: 36653863 PMCID: PMC9850602 DOI: 10.1186/s13007-023-00983-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Cotton has tremendous economic value worldwide; however, its allopolyploid nature and time-consuming transformation methods have hampered the development of cotton functional genomics. The protoplast system has proven to be an important and versatile tool for functional genomics, tissue-specific marker gene identification, tracking developmental trajectories, and genome editing in plants. Nevertheless, the isolation of abundant viable protoplasts suitable for single-cell RNA sequencing (scRNA-seq) and genome editing remains a challenge in cotton. RESULTS We established an efficient transient gene expression system using protoplasts isolated from cotton taproots. The system enables the isolation of large numbers of viable protoplasts and uses an optimized PEG-mediated transfection protocol. The highest yield (3.55 × 105/g) and viability (93.3%) of protoplasts were obtained from cotton roots grown in hydroponics for 72 h. The protoplasts isolated were suitable for scRNA-seq. The highest transfection efficiency (80%) was achieved when protoplasts were isolated as described above and transfected with 20 μg of plasmid for 20 min in a solution containing 200 mM Ca2+. Our protoplast-based transient expression system is suitable for various applications, including validation the efficiency of CRISPR vectors, protein subcellular localization analysis, and protein-protein interaction studies. CONCLUSIONS The protoplast isolation and transfection protocol developed in this study is stable, versatile, and time-saving. It will accelerate functional genomics and molecular breeding in cotton.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Shanhe Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Yunze Fu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Zixuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071001, China
| | - Xiubo Yang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Wenjing Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Caihua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
- Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071001, China.
| | - Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China.
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19
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Das J, Kumar S, Mishra DC, Chaturvedi KK, Paul RK, Kairi A. Machine learning in the estimation of CRISPR-Cas9 cleavage sites for plant system. Front Genet 2023; 13:1085332. [PMID: 36699447 PMCID: PMC9868961 DOI: 10.3389/fgene.2022.1085332] [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: 10/31/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
CRISPR-Cas9 system is one of the recent most used genome editing techniques. Despite having a high capacity to alter the precise target genes and genomic regions that the planned guide RNA (or sgRNA) complements, the off-target effect still exists. But there are already machine learning algorithms for people, animals, and a few plant species. In this paper, an effort has been made to create models based on three machine learning-based techniques [namely, artificial neural networks (ANN), support vector machines (SVM), and random forests (RF)] for the prediction of the CRISPR-Cas9 cleavage sites that will be cleaved by a particular sgRNA. The plant dataset was the sole source of inspiration for all of these machine learning-based algorithms. 70% of the on-target and off-target dataset of various plant species that was gathered was used to train the models. The remaining 30% of the data set was used to evaluate the model's performance using a variety of evaluation metrics, including specificity, sensitivity, accuracy, precision, F1 score, F2 score, and AUC. Based on the aforementioned machine learning techniques, eleven models in all were developed. Comparative analysis of these produced models suggests that the model based on the random forest technique performs better. The accuracy of the Random Forest model is 96.27%, while the AUC value was found to be 99.21%. The SVM-Linear, SVM-Polynomial, SVM-Gaussian, and SVM-Sigmoid models were trained, making a total of six ANN-based models (ANN1-Logistic, ANN1-Tanh, ANN1-ReLU, ANN2-Logistic, ANN2-Tanh, and ANN-ReLU) and Support Vector Machine models (SVM-Linear, SVM-Polynomial, SVM-Gaussian However, the overall performance of Random Forest is better among all other ML techniques. ANN1-ReLU and SVM-Linear model performance were shown to be better among Artificial Neural Network and Support Vector Machine-based models, respectively.
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Affiliation(s)
- Jutan Das
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjeev Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India,*Correspondence: Sanjeev Kumar,
| | | | | | - Ranjit Kumar Paul
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amit Kairi
- ICAR-Indian Agricultural Research Institute, New Delhi, India
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20
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Kumar M, Prusty MR, Pandey MK, Singh PK, Bohra A, Guo B, Varshney RK. Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1157678. [PMID: 37143874 PMCID: PMC10153630 DOI: 10.3389/fpls.2023.1157678] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reducing global agricultural production. Traditional breeding approaches and transgenic technology have been widely used to mitigate the risks of these environmental stresses. The discovery of engineered nucleases as genetic scissors to carry out precise manipulation in crop stress-responsive genes and associated molecular network has paved the way for sustainable management of abiotic stress conditions. In this context, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas)-based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the latest findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas-mediated gene-editing system towards enhanced tolerance to a multitude of stresses including drought, salinity, cold, heat, and heavy metals. We provide mechanistic insights on the CRISPR/Cas9-based genome editing technology. We also discuss applications of evolving genome editing techniques such as prime editing and base editing, mutant library production, transgene free and multiplexing to rapidly deliver modern crop cultivars adapted to abiotic stress conditions.
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Affiliation(s)
- Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
| | - Manas Ranjan Prusty
- Institute for Cereal Crop Improvement, Plant Science, Tel Aviv University, Tel Aviv, Israel
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College, Aizawl, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Baozhu Guo
- Crop Genetics and Breeding Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA, United States
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ; Baozhu Guo, ; Manoj Kumar,
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21
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Zhou L, Wang Y, Wang P, Wang C, Wang J, Wang X, Cheng H. Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene editing analysis in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1059404. [PMID: 36643290 PMCID: PMC9832336 DOI: 10.3389/fpls.2022.1059404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
CRIPSR/Cas9 gene editing system is an effective tool for genome modification in plants. Multiple target sites are usually designed and the effective target sites are selected for editing. Upland cotton (Gossypium hirsutum L., hereafter cotton) is allotetraploid and is commonly considered as difficult and inefficient to transform, it is important to select the effective target sites that could result in the ideal transgenic plants with the CRISPR-induced mutations. In this study, Agrobacterium rhizogenes-mediated hairy root method was optimized to detect the feasibility of the target sites designed in cotton phytoene desaturase (GhPDS) gene. A. rhizogenes showed the highest hairy root induction (30%) when the bacteria were cultured until OD600 reached to 0.8. This procedure was successfully applied to induce hairy roots in the other three cultivars (TM-1, Lumian-21, Zhongmian-49) and the mutations were detected in GhPDS induced by CRISPR/Cas9 system. Different degrees of base deletions at two sgRNAs (sgRNA5 and sgRNA10) designed in GhPDS were detected in R15 hairy roots. Furthermore, we obtained an albino transgenic cotton seeding containing CRISPR/Cas9-induced gene editing mutations in sgRNA10. The hairy root transformation system established in this study is sufficient for selecting sgRNAs in cotton, providing a technical basis for functional genomics research of cotton.
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Affiliation(s)
- Lili Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yali Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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22
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Song GQ, Urban G, Ryner JT, Zhong GY. Gene Editing Profiles in 94 CRISPR-Cas9 Expressing T 0 Transgenic Tobacco Lines Reveal High Frequencies of Chimeric Editing of the Target Gene. PLANTS (BASEL, SWITZERLAND) 2022; 11:3494. [PMID: 36559603 PMCID: PMC9782292 DOI: 10.3390/plants11243494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Chimeric editing is often reported in gene editing. To assess how the general chimeric editing is, we created a transgenic tobacco line carrying a marker, beta-glucuronidase gene (gusA), introduced a CRISPR-Cas9 editing vector into the transgenic tobacco line for knocking out gusA, and then investigated the gusA editing efficiencies in T0 and subsequent generations. The editing vector carried a Cas9 gene, which was driven by the cauliflower mosaic virus 35S promoter, and two guide RNAs, gRNA1 and gRNA2, which were driven by Arabidopsis U6 (AtU6) and U3 (AtU3) promoter, respectively. The two gRNAs were designed to knock out a 42-nucleotide fragment of the coding region of gusA. The editing vector was transformed into gusA-containing tobacco leaves using Agrobacterium tumefaciens-mediated transformation and hygromycin selection. Hygromycin-resistant, independent T0 transgenic lines were used to evaluate gusA-editing efficiencies through histochemical GUS assays, polymerase chain reactions (PCR), and next-generation sequencing of PCR amplicons. Profiles of targeted sequences of 94 T0 transgenic lines revealed that these lines were regenerated from non-edited cells where subsequent editing occurred and created chimeric-edited cells in these lines during or after regeneration. Two of them had the target fragment of 42 bp pairs of nucleotides removed. Detail analysis showed that on-target mutations at the AtU6-gRNA1 site and the AtU3-gRNA2 site were found in 4.3% and 77.7% of T0 transgenic lines, respectively. To overcome the issue of extremely low editing efficiencies in T0 lines, we conducted a second round of shoot induction from the chimeric line(s) to enhance the success of obtaining lines with all or most cells edited. The mutation profiles in T0 transgenic lines provide valuable information to understand gene editing in plant cells with constitutively expressed CRISPR-Cas9 and gRNAs.
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Affiliation(s)
- Guo-Qing Song
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Grace Urban
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - John T. Ryner
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Gan-Yuan Zhong
- Grape Genetics Research Unit, USDA-Agricultural Research Service, Geneva, NY 14456, USA
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23
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Lei J, Li Y, Dai P, Liu C, Zhao Y, You Y, Qu Y, Chen Q, Liu X. Efficient virus-mediated genome editing in cotton using the CRISPR/Cas9 system. FRONTIERS IN PLANT SCIENCE 2022; 13:1032799. [PMID: 36466231 PMCID: PMC9709312 DOI: 10.3389/fpls.2022.1032799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Plant virus-mediated sgRNA delivery and expression have great advantages; sgRNA expression can rapidly expand and accumulate along with virus replication and movement, resulting in efficient gene editing efficiency. In this study, a VIGE system based on cotton leaf crumple virus (CLCrV) was established using cotton overexpressing Cas9 (Cas9-OE) as the VIGE receptor. CLCrV-mediated VIGE could not only target and knock out the GhMAPKKK2, GhCLA1 and GhPDS genes subgroup A and D genome sequences but also achieve double mutation of GhCLA1 and GhPDS genes at the same time. These results verified the effectiveness and efficiency of this system. In addition, the off-target effect assay demonstrated that the CLCrV-mediated VIGE system not only has high gene editing efficiency but also high gene editing specificity in cotton. We further explored whether the FT-sgRNA strategy could transport sgRNA to cotton apical meristem (SAM) over long distances to avoid using tissue culture to obtain stable genetic mutants. The results showed that the sgRNA fused with FT mRNA at the 5' end could also efficiently achieve targeted editing of endogenous genes in cotton, but it was difficult to detect heritable mutant progeny. The above results showed that the CLCrV-mediated VIGE system provided an accurate and rapid validation tool for screening effective sgRNAs in cotton.
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Affiliation(s)
- Jianfeng Lei
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Yue Li
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Peihong Dai
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Chao Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yi Zhao
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yangzi You
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Xiaodong Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
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24
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Sharma KK, Palakolanu SR, Bhattacharya J, Shankhapal AR, Bhatnagar-Mathur P. CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects. Front Genet 2022; 13:999207. [PMID: 36276961 PMCID: PMC9582247 DOI: 10.3389/fgene.2022.999207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.
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Affiliation(s)
- Kiran K. Sharma
- Sustainable Agriculture Programme, The Energy and Resources Institute (TERI), India Habitat Center, New Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Aishwarya R. Shankhapal
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- International Maize and Wheat Improvement Center (CIMMYT), México, United Kingdom
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25
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Biswas S, Ibarra O, Shaphek M, Molina-Risco M, Faion-Molina M, Bellinatti-Della Gracia M, Thomson MJ, Septiningsih EM. Increasing the level of resistant starch in 'Presidio' rice through multiplex CRISPR-Cas9 gene editing of starch branching enzyme genes. THE PLANT GENOME 2022:e20225. [PMID: 35713092 DOI: 10.1002/tpg2.20225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is an excellent source of starch, which is composed of amylopectin and amylose. Resistant starch (RS) is a starch product that is not easily digestible and absorbed in the stomach or small intestine and instead is passed on directly to the large intestine. Cereals high in RS may be beneficial to improve human health and reduce the risk of diet-related chronic diseases. It has been reported through chemical mutagenesis and RNA interference studies that starch branching enzymes (SBEs) play a major role in contributing to higher levels of RS in cereal crops. In this study, we used multiplex clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) genome editing to simultaneously target all four SBE genes in rice using the endogenous transfer RNA (tRNA)-processing system for expressing the single-guide RNAs (sgRNAs) targeting these genes. The CRISPR-Cas9 vector construct with four SBE gene sgRNAs was transformed into the U.S. rice cultivar Presidio using Agrobacterium-mediated transformation. Knockout mutations were identified at all four SBE genes across eight transgene-positive T0 plants. Transgene-free T1 lines with different combinations of disrupted SBE genes were identified, with several SBE-edited lines showing significantly increased RS content up to 15% higher than the wild-type (WT) cultivar Presidio. Although further efforts are needed to fix all of the mutant alleles as homozygous, our study demonstrated the potential of multiplex genome editing to develop high-RS lines.
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Affiliation(s)
- Sudip Biswas
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Oneida Ibarra
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Avance Biosciences Inc., Houston, TX, 77040, USA
| | - Mariam Shaphek
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Dep. of Biochemistry and Biophysics, Texas A&M Univ., College Station, TX, 77843, USA
| | - Marco Molina-Risco
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Mayra Faion-Molina
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | | | - Michael J Thomson
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
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26
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Viviani A, Spada M, Giordani T, Fambrini M, Pugliesi C. Origin of the genome editing systems: application for crop improvement. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses. Curr Issues Mol Biol 2022; 44:2664-2682. [PMID: 35735623 PMCID: PMC9221872 DOI: 10.3390/cimb44060182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Global warming and climate change have severely affected plant growth and food production. Therefore, minimizing these effects is required for sustainable crop yields. Understanding the molecular mechanisms in response to abiotic stresses and improving agricultural traits to make crops tolerant to abiotic stresses have been going on unceasingly. To generate desirable varieties of crops, traditional and molecular breeding techniques have been tried, but both approaches are time-consuming. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALENs) are genome-editing technologies that have recently attracted the attention of plant breeders for genetic modification. These technologies are powerful tools in the basic and applied sciences for understanding gene function, as well as in the field of crop breeding. In this review, we focus on the application of genome-editing systems in plants to understand gene function in response to abiotic stresses and to improve tolerance to abiotic stresses, such as temperature, drought, and salinity stresses.
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28
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Sharwood RE, Quick WP, Sargent D, Estavillo GM, Silva-Perez V, Furbank RT. Mining for allelic gold: finding genetic variation in photosynthetic traits in crops and wild relatives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3085-3108. [PMID: 35274686 DOI: 10.1093/jxb/erac081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large 'gene bank' collections of germplasm comprising historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programmes. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes, and deployment of this variation via gene editing in modern elite material.
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Affiliation(s)
- Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - W Paul Quick
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Demi Sargent
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | | | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
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29
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Supriya L, Durgeshwar P, Muthamilarasan M, Padmaja G. Melatonin Mediated Differential Regulation of Drought Tolerance in Sensitive and Tolerant Varieties of Upland Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:821353. [PMID: 35444676 PMCID: PMC9014207 DOI: 10.3389/fpls.2022.821353] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/17/2022] [Indexed: 05/28/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine), a biomolecule with multifunctional phyto-protectant activities, enhances the tolerance to broad-spectrum biotic and abiotic stresses in plants. However, little information is available on the effect of melatonin on different morpho-physiological, biochemical, and molecular parameters during drought stress incidence in varieties contrastingly differing in their tolerance levels. The present study is aimed at investigating the drought stress responses of drought-sensitive (var. L-799) and drought-tolerant (var. Suraj) varieties after exogenous melatonin priming and gaining mechanistic insights into drought tolerance in upland cotton (Gossypium hirsutum). Melatonin-priming enhanced the tolerance of L-799 to drought stress by modulating the antioxidant system, with increased photosynthetic activity, water-use efficiency, and nitrogen metabolism. Higher endogenous melatonin content and upregulated expression of candidate stress-responsive genes in primed L-799 suggested their involvement in drought tolerance. The higher expression of autophagosome marker [lipidated (ATG8-PE)] in melatonin-primed drought-stressed plants of L-799 also indicated the role of autophagy in alleviating drought stress. Interestingly, melatonin-priming did not show pronounced differences in the different parameters studied during the presence or absence of drought stress in Suraj. In conclusion, this study showed that melatonin plays an important role in mitigating drought stress effects by modulating several physiological, biochemical, and molecular processes, with the key regulatory factor being the plant tolerance level that serves as the switch that turns the priming effects on/off.
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Affiliation(s)
| | | | | | - Gudipalli Padmaja
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Bharathkumar N, Sunil A, Meera P, Aksah S, Kannan M, Saravanan KM, Anand T. CRISPR/Cas-Based Modifications for Therapeutic Applications: A Review. Mol Biotechnol 2022; 64:355-372. [PMID: 34741732 PMCID: PMC8571677 DOI: 10.1007/s12033-021-00422-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022]
Abstract
The CRISPR-Cas genome editing system is an intrinsic property of a bacteria-based immune system. This employs a guide RNA to detect and cleave the PAM-associated target DNA or RNA in subsequent infections, by the invasion of a similar bacteriophage. The discovery of Cas systems has paved the way to overcome the limitations of existing genome editing tools. In this review, we focus on Cas proteins that are available for gene modifications among which Cas9, Cas12a, and Cas13 have been widely used in the areas of medicine, research, and diagnostics. Since CRISPR has been already proven for its potential research applications, the next milestone for CRISPR will be proving its efficacy and safety. In this connection, we systematically review recent advances in exploring multiple variants of Cas proteins and their modifications for therapeutic applications.
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Affiliation(s)
| | - Abraham Sunil
- Department of Animal Behavior and Physiology, Madurai Kamaraj University, Madurai, Tamil Nadu India
| | - Prabhakar Meera
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Sam Aksah
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Muthu Kannan
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
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Wang L, Wang Y, Makhmoudova A, Nitschke F, Tetlow IJ, Emes MJ. CRISPR-Cas9-mediated editing of starch branching enzymes results in altered starch structure in Brassica napus. PLANT PHYSIOLOGY 2022; 188:1866-1886. [PMID: 34850950 PMCID: PMC8968267 DOI: 10.1093/plphys/kiab535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 05/24/2023]
Abstract
Starch branching enzymes (SBEs) are one of the major classes of enzymes that catalyze starch biosynthesis in plants. Here, we utilized the clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9)-mediated gene editing system to investigate the effects of SBE mutation on starch structure and turnover in the oilseed crop Brassica napus. Multiple single-guide RNA (sgRNA) expression cassettes were assembled into a binary vector and two rounds of transformation were employed to edit all six BnaSBE genes. All mutations were heterozygous monoallelic or biallelic, and no chimeric mutations were detected from a total of 216 editing events. Previously unannotated gene duplication events associated with two BnaSBE genes were characterized through analysis of DNA sequencing chromatograms, reflecting the complexity of genetic information in B. napus. Five Cas9-free homozygous mutant lines carrying two to six mutations of BnaSBE were obtained, allowing us to compare the effect of editing different BnaSBE isoforms. We also found that in the sextuple sbe mutant, although indels were introduced at the genomic DNA level, an alternate transcript of one BnaSBE2.1 gene bypassed the indel-induced frame shift and was translated to a modified full-length protein. Subsequent analyses showed that the sextuple mutant possesses much lower SBE enzyme activity and starch branching frequency, higher starch-bound phosphate content, and altered pattern of amylopectin chain length distribution relative to wild-type (WT) plants. In the sextuple mutant, irregular starch granules and a slower rate of starch degradation during darkness were observed in rosette leaves. At the pod-filling stage, the sextuple mutant was distinguishable from WT plants by its thick main stem. This work demonstrates the applicability of the CRISPR-Cas9 system for the study of multi-gene families and for investigation of gene-dosage effects in the oil crop B. napus. It also highlights the need for rigorous analysis of CRISPR-Cas9-mutated plants, particularly with higher levels of ploidy, to ensure detection of gene duplications.
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Affiliation(s)
| | - You Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Amina Makhmoudova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Felix Nitschke
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Hu GY, Ma JY, Li F, Zhao JR, Xu FC, Yang WW, Yuan M, Gao W, Long L. Optimizing the Protein Fluorescence Reporting System for Somatic Embryogenesis Regeneration Screening and Visual Labeling of Functional Genes in Cotton. FRONTIERS IN PLANT SCIENCE 2022; 12:825212. [PMID: 35069674 PMCID: PMC8777222 DOI: 10.3389/fpls.2021.825212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Protein fluorescence reporting systems are of crucial importance to in-depth life science research, providing systematic labeling tools for visualization of microscopic biological activities in vivo and revolutionizing basic research. Cotton somatic cell regeneration efficiency is low, causing difficulty in cotton transformation. It is conducive to screening transgenic somatic embryo using the fluorescence reporting system. However, available fluorescence labeling systems in cotton are currently limited. To optimize the fluorescence reporting system of cotton with an expanded range of available fluorescent proteins, we selected 11 fluorescent proteins covering red, green, yellow, and cyan fluorescence colors and expressed them in cotton. Besides mRuby2 and G3GFP, the other nine fluorescent proteins (mCherry, tdTomato, sfGFP, Clover, EYFP, YPet, mVenus, mCerulean, and ECFP) were stably and intensely expressed in transgenic callus and embryo, and inherited in different cotton organs derive from the screened embryo. In addition, transgenic cotton expressing tdTomato appears pink under white light, not only for callus and embryo tissues but also various organs of mature plants, providing a visual marker in the cotton genetic transformation process, accelerating the evaluation of transgenic events. Further, we constructed transgenic cotton expressing mCherry-labeled organelle markers in vivo that cover seven specific subcellular compartments: plasma membrane, endoplasmic reticulum, tonoplast, mitochondrion, plastid, Golgi apparatus, and peroxisome. We also provide a simple and highly efficient strategy to quickly determine the subcellular localization of uncharacterized proteins in cotton cells using organelle markers. Lastly, we built the first cotton stomatal fluorescence reporting system using stomata-specific expression promoters (ProKST1, ProGbSLSP, and ProGC1) to drive Clover expression. The optimized fluorescence labeling system for transgenic somatic embryo screening and functional gene labeling in this study offers the potential to accelerating somatic cell regeneration efficiency and the in vivo monitoring of diverse cellular processes in cotton.
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Affiliation(s)
- Gai-Yuan Hu
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jia-Yi Ma
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Fen Li
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jing-Ruo Zhao
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Wen-Wen Yang
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Man Yuan
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Wei Gao
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
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Hussain Y, Khan H, Ahmad I, Efferth T, Alam W. Nanoscale delivery of phytochemicals targeting CRISPR/Cas9 for cancer therapy. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 94:153830. [PMID: 34775359 DOI: 10.1016/j.phymed.2021.153830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND With growing global prevalence, cancer is a major cause of disease-related deaths. The understanding of the fundamental tumor pathology has contributed to the development of agents targeting oncogenic signaling pathways. Although these agents have increased survival for defined cancers, the therapeutic choices are still limited due to the development of drug resistance. CRISPR/Cas9 is a powerful new technology in cancer therapy by facilitating the identification of novel treatment targets and development of cell-based treatment strategies. PURPOSE We focused on applications of the CRISPR/Cas9 system in cancer therapy and discuss nanoscale delivery of cytotoxic phytochemical targeting the CRISPR/Cas9 system. RESULTS Genome engineering has been significantly accelerated by the advancement of the CRISPR/Cas9 technique. Phytochemicals play a key role in treating cancer by targeting various mechanisms and pathways. CONCLUSIONS The use of CRISPR/Cas9 for nanoscale delivery of phytochemicals opens new avenues in cancer therapy. One of the main obstacles in the clinical application of CRISPR/Cas9 is safe and efficient delivery. As viral delivery methods have certain drawbacks, there is an urgent need to develop non-viral delivery systems for therapeutic applications.
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Affiliation(s)
- Yaseen Hussain
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Haroon Khan
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan.
| | - Imad Ahmad
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
| | - Waqas Alam
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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36
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Niu F, Jiang Q, Sun X, Hu Z, Wang L, Zhang H. Large DNA fragment deletion in lncRNA77580 regulates neighboring gene expression in soybean (Glycine max). FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1139-1147. [PMID: 34585661 DOI: 10.1071/fp20400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) affect gene expressions via a wide range of mechanisms and are considered important regulators of numerous essential biological processes, including abiotic stress responses. However, the biological functions of most lncRNAs are yet to be determined. Moreover, to date, no effective methods have been developed to study the function of plant lncRNAs. We previously discovered a salt stress-related lncRNA, lncRNA77580 in soybean (Glycine max L.). In this study, we cloned the full-length lncRNA77580 and found that it shows nuclear-specific localisation. Furthermore, we employed CRISPR/Cas9 technology to induce large DNA fragment deletions in lncRNA77580 in soybean using a dual-single guide RNA/Cas9 design. As a result, we obtained deletion mutant soybean roots with targeted genomic fragment deletion in lncRNA77580. Deletion and overexpression of lncRNA77580 were found to alter the expression of several neighboring protein-coding genes associated with the response to salt stress. The longer the deleted DNA fragment in lncRNA77580, the greater the influence on the expression of lncRNA77580 itself and neighboring genes. Collectively, the findings of this study revealed that large DNA fragment deletion in lncRNAs using the CRISPR/Cas9 system is a powerful method to obtain functional mutations of soybean lncRNAs that could benefit future research on lncRNA function in soybean.
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Affiliation(s)
- Fengjuan Niu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | | | - Xianjun Sun
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zheng Hu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lixia Wang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Hao W, Cui W, Cheng Z, Han L, Suo F, Liu Z, Zhou L, Zhou Z. Development of a base editor for protein evolution via in situ mutation in vivo. Nucleic Acids Res 2021; 49:9594-9605. [PMID: 34390349 PMCID: PMC8450078 DOI: 10.1093/nar/gkab673] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022] Open
Abstract
Protein evolution has significantly enhanced the development of life science. However, it is difficult to achieve in vitro evolution of some special proteins because of difficulties with heterologous expression, purification, and function detection. To achieve protein evolution via in situ mutation in vivo, we developed a base editor by fusing nCas with a cytidine deaminase in Bacillus subtilis through genome integration. The base editor introduced a cytidine-to-thymidine mutation of approximately 100% across a 5 nt editable window, which was much higher than those of other base editors. The editable window was expanded to 8 nt by extending the length of sgRNA, and conversion efficiency could be regulated by changing culture conditions, which was suitable for constructing a mutant protein library efficiently in vivo. As proof-of-concept, the Sec-translocase complex and bacitracin-resistance-related protein BceB were successfully evolved in vivo using the base editor. A Sec mutant with 3.6-fold translocation efficiency and the BceB mutants with different sensitivity to bacitracin were obtained. As the construction of the base editor does not rely on any additional or host-dependent factors, such base editors (BEs) may be readily constructed and applicable to a wide range of bacteria for protein evolution via in situ mutation.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongyi Cheng
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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Miladinovic D, Antunes D, Yildirim K, Bakhsh A, Cvejić S, Kondić-Špika A, Marjanovic Jeromela A, Opsahl-Sorteberg HG, Zambounis A, Hilioti Z. Targeted plant improvement through genome editing: from laboratory to field. PLANT CELL REPORTS 2021; 40:935-951. [PMID: 33475781 PMCID: PMC8184711 DOI: 10.1007/s00299-020-02655-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/20/2020] [Indexed: 05/19/2023]
Abstract
This review illustrates how far we have come since the emergence of GE technologies and how they could be applied to obtain superior and sustainable crop production. The main challenges of today's agriculture are maintaining and raising productivity, reducing its negative impact on the environment, and adapting to climate change. Efficient plant breeding can generate elite varieties that will rapidly replace obsolete ones and address ongoing challenges in an efficient and sustainable manner. Site-specific genome editing in plants is a rapidly evolving field with tangible results. The technology is equipped with a powerful toolbox of molecular scissors to cut DNA at a pre-determined site with different efficiencies for designing an approach that best suits the objectives of each plant breeding strategy. Genome editing (GE) not only revolutionizes plant biology, but provides the means to solve challenges related to plant architecture, food security, nutrient content, adaptation to the environment, resistance to diseases and production of plant-based materials. This review illustrates how far we have come since the emergence of these technologies and how these technologies could be applied to obtain superior, safe and sustainable crop production. Synergies of genome editing with other technological platforms that are gaining significance in plants lead to an exciting new, post-genomic era for plant research and production. In previous months, we have seen what global changes might arise from one new virus, reminding us of what drastic effects such events could have on food production. This demonstrates how important science, technology, and tools are to meet the current time and the future. Plant GE can make a real difference to future sustainable food production to the benefit of both mankind and our environment.
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Affiliation(s)
| | | | - Kubilay Yildirim
- Department of Molecular Biology and Genetics, Faculty of Sciences, Ondokuzmayıs University, Samsun, Turkey
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Sandra Cvejić
- Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | | | | | | | - Antonios Zambounis
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER, Naoussa, Greece
| | - Zoe Hilioti
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.
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Numan M, Serba DD, Ligaba-Osena A. Alternative Strategies for Multi-Stress Tolerance and Yield Improvement in Millets. Genes (Basel) 2021; 12:genes12050739. [PMID: 34068886 PMCID: PMC8156724 DOI: 10.3390/genes12050739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity in marginal environments and will help in overcoming future food shortage due to climate change. Recently, approaches such as application of plant growth-promoting rhizobacteria (PGPRs) have been used to improve growth and development, as well as stress tolerance of crops. Moreover, with the advance of next-generation sequencing technology, genome editing, using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system are increasingly used to develop stress tolerant varieties in different crops. In this paper, the innate ability of millets to tolerate abiotic stresses and alternative approaches to boost stress resistance were thoroughly reviewed. Moreover, several stress-resistant genes were identified in related monocots such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), and other related species for which orthologs in millets could be manipulated by CRISPR/Cas9 and related genome-editing techniques to improve stress resilience and productivity. These cutting-edge alternative strategies are expected to bring this group of orphan crops at the forefront of scientific research for their potential contribution to global food security.
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Affiliation(s)
- Muhammad Numan
- Laboratory of Biotechnology and Molecular Biology, Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27412, USA;
| | - Desalegn D. Serba
- USDA-ARS, U. S. Arid-Land Agricultural Research Center, 21881 N Cardon Ln., Maricopa, AZ 85138, USA;
| | - Ayalew Ligaba-Osena
- Laboratory of Biotechnology and Molecular Biology, Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27412, USA;
- Correspondence:
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Lei J, Dai P, Li Y, Zhang W, Zhou G, Liu C, Liu X. Heritable gene editing using FT mobile guide RNAs and DNA viruses. PLANT METHODS 2021; 17:20. [PMID: 33596981 PMCID: PMC7890912 DOI: 10.1186/s13007-021-00719-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/06/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The virus-induced genome editing (VIGE) system can be used to quickly identify gene functions and generate knock-out libraries as an alternative to the virus-induced gene silencing (VIGS). Although plant virus-mediated VIGE has been shown to have great application prospects, edited genes cannot be transferred to the next generations using this system, as viruses cannot enter into shoot apical meristem (SAM) in plants. RESULTS We developed a novel cotton leaf crumple virus (CLCrV)-mediated VIGE system designed to target BRI1, GL2, PDS genes, and GUS transgene in A. thaliana by transforming Cas9 overexpression (Cas9-OE) A. thaliana. Given the deficiency of the VIGE system, ProYao::Cas9 and Pro35S::Cas9 A. thaliana were transformed by fusing 102 bp FT mRNAs with sgRNAs so as to explore the function of Flowering Locus T (FT) gene in delivering sgRNAs into SAM, thus avoiding tissue culture and stably acquiring heritable mutant offspring. Our results showed that sgRNAs fused with FT mRNA at the 5' end (FT strategy) effectively enabled gene editing in infected plants and allowed the acquisition of mutations heritable by the next generation, with an efficiency of 4.35-8.79%. In addition, gene-edited offspring by FT-sgRNAs did not contain any components of the CLCrV genome. CONCLUSIONS FT strategy can be used to acquire heritable mutant offspring avoiding tissue culture and stable transformation based on the CLCrV-mediated VIGE system in A. thaliana.
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Affiliation(s)
- Jianfeng Lei
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Peihong Dai
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Yue Li
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Wanqi Zhang
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Guantong Zhou
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Chao Liu
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China
| | - Xiaodong Liu
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, 311 Nongda East Road, Urumqi, 830052, P.R. China.
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Ramadan M, Alariqi M, Ma Y, Li Y, Liu Z, Zhang R, Jin S, Min L, Zhang X. Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton. PLANT METHODS 2021; 17:16. [PMID: 33557889 PMCID: PMC7869495 DOI: 10.1186/s13007-021-00712-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. RESULTS To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. CONCLUSION All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.
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Affiliation(s)
- Mohamed Ramadan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Plant Genetic Resources, Division of Ecology and Dry Land Agriculture, Desert Research Center, Cairo, Egypt
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
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Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
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Tyagi S, Kumar R, Kumar V, Won SY, Shukla P. Engineering disease resistant plants through CRISPR-Cas9 technology. GM CROPS & FOOD 2021; 12:125-144. [PMID: 33079628 PMCID: PMC7583490 DOI: 10.1080/21645698.2020.1831729] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/13/2020] [Accepted: 09/27/2020] [Indexed: 01/08/2023]
Abstract
Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.
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Affiliation(s)
- Swati Tyagi
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Robin Kumar
- Department of Soil Science and Agricultural Chemistry, Acharya Narendra Dev University of Agriculture and Technology, Kumarganj, Ayodhya, India
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - Vivak Kumar
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - So Youn Won
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Zhang Y, Restall J, Crisp P, Godwin I, Liu G. Current status and prospects of plant genome editing in Australia. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2021; 57:574-583. [PMID: 34054265 PMCID: PMC8143062 DOI: 10.1007/s11627-021-10188-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/13/2021] [Indexed: 05/22/2023]
Abstract
Plant genome editing, particularly CRISPR-Cas biotechnologies, has rapidly evolved and drawn enormous attention all around the world in the last decade. The cutting-edge technologies have had substantial impact on precise genome editing for manipulating gene expression, stacking gene mutations, and improving crop agronomic traits. Following the global trends, investigations on CRISPR-Cas have been thriving in Australia, especially in agriculture sciences. Importantly, CRISPR-edited plants, classified as SDN-1 organisms (SDN: site-directed nuclease), have been given a green light in Australia, with regulatory bodies indicating they will not be classified as a genetically modified organism (GMO) if no foreign DNA is present in an edited plant. As a result, genome-edited products would not attract the onerous regulation required for the introduction of a GMO, which could mean more rapid deployment of new varieties and products that could be traded freely in Australia, and potentially to export markets. In the present review, we discuss the current status and prospects of plant genome editing in Australia by highlighting several species of interest. Using these species as case studies, we discuss the priorities and potential of plant genome editing, as well as the remaining challenges.
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Affiliation(s)
- Yan Zhang
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Jemma Restall
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Peter Crisp
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Ian Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Guoquan Liu
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072 Australia
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Abstract
Energy security and climate change have cascading effects on the world's burgeoning population in terms of food security, environment, and sustainability. Due to depletion of fossil fuels and undesirable changes of climatic conditions, increase in air and water pollution, mankind started exploring alternate and sustainable means of meeting growing energy needs. One of the options is to use renewable sources of fuel-biofuel. In this chapter the authors have reviewed and presented sustainability impact on production of biofuels. Authors further reviewed state-of-the-art gene editing technologies toward improvement of biofuel crops. The authors recommend a phased transition from first-generation biofuel, and an acceleration toward use of technology to drive adoption of second-generation biofuels. Key aspects of technology and application of resource management models will enable these crops to bridge the global energy demand before we can completely transition to a more sustainable biofuel economy.
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48
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Wenjing W, Chen Q, Singh PK, Huang Y, Pei D. CRISPR/Cas9 edited HSFA6a and HSFA6b of Arabidopsis thaliana offers ABA and osmotic stress insensitivity by modulation of ROS homeostasis. PLANT SIGNALING & BEHAVIOR 2020; 15:1816321. [PMID: 32936726 PMCID: PMC7671043 DOI: 10.1080/15592324.2020.1816321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 05/21/2023]
Abstract
The role of Heat Shock Transcription Factor 6 (HSFA6a & HSFA6b) in response to abiotic stresses such as ABA, drought, salinity, drought, and osmotic stress is individually well established. Unfortunately, the functional redundancy between the HSFA6a and HSFA6b as well as the consequences of simultaneous editing of both in response to aforementioned stresses remains elusive. Therefore, this study was designed with the aim of addressing whether there is any functional redundancy between HSFA6a and HSFA6b as well as to decipher their role in abiotic stresses tolerance in Arabidopsis thaliana, by using the CRISPR-Cas9. We have generated the single (hsfa6a and hsfa6b) as well as double mutants (hsfa6a/hsfa6b-1 and hsfa6a/hsfa6b-2) of HSFA6a and HSFA6b with higher frequencies of deletion, insertion, and substitution. The phenotypic characterization of generated double and single mutants under abiotic stresses such as ABA, mannitol, and NaCl identified double mutants more tolerant to subjected abiotic stresses than those of their single mutants. It warrants mentioning that we have identified that HSFA6a and HSFA6b also involved in other major ABA responses, including ABA-inhibited seed germination, stomatal movement, and water loss. In addition to the above, the simultaneous editing of HSFA6a and HSFA6b lead to a reduced ROS accumulation, accompanied by increased expression of much abiotic stress and ABA-responsive genes, including involved in regulation of ROS level. In conclusion, these results suggest that HSFA6a and HSFA6b may offer abiotic stress tolerance by regulating the ROS homeostasis in plants.
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Affiliation(s)
- Wang Wenjing
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
| | - Qingbin Chen
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
| | - Prashant Kumar Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, Henan, China
- Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, India
| | - Yuanyuan Huang
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
| | - Dongli Pei
- Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, China
- CONTACT Dongli Pei Department of Biology and Food Science, Shangqiu Normal University, Shangqiu, Henan, 476000, China
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López-Marqués RL, Nørrevang AF, Ache P, Moog M, Visintainer D, Wendt T, Østerberg JT, Dockter C, Jørgensen ME, Salvador AT, Hedrich R, Gao C, Jacobsen SE, Shabala S, Palmgren M. Prospects for the accelerated improvement of the resilient crop quinoa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5333-5347. [PMID: 32643753 PMCID: PMC7501820 DOI: 10.1093/jxb/eraa285] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/11/2020] [Indexed: 05/04/2023]
Abstract
Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.
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Affiliation(s)
- Rosa L López-Marqués
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Correspondence: or
| | - Anton F Nørrevang
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Max Moog
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Davide Visintainer
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Jeppe T Østerberg
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Andrés Torres Salvador
- The Quinoa Company, Wageningen, The Netherlands
- Plant Biotechnology Laboratory (COCIBA), Universidad San Francisco de Quito USFQ, Cumbayá, Ecuador
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Correspondence: or
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50
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Hao W, Suo F, Lin Q, Chen Q, Zhou L, Liu Z, Cui W, Zhou Z. Design and Construction of Portable CRISPR-Cpf1-Mediated Genome Editing in Bacillus subtilis 168 Oriented Toward Multiple Utilities. Front Bioeng Biotechnol 2020; 8:524676. [PMID: 32984297 PMCID: PMC7492563 DOI: 10.3389/fbioe.2020.524676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Bacillus subtilis is an important Gram-positive bacterium for industrial biotechnology, which has been widely used to produce diverse high-value added chemicals and industrially and pharmaceutically relevant proteins. Robust and versatile toolkits for genome editing in B. subtilis are highly demanding to design higher version chassis. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 has been extensively adapted for genome engineering of multiple bacteria, it has many defects, such as higher molecular weight which leads to higher carrier load, low deletion efficiency and complexity of sgRNA construction for multiplex genome editing. Here, we designed a CRISPR-Cpf1-based toolkit employing a type V Cas protein, Cpf1 from Francisella novicida. Using this platform, we precisely deleted single gene and gene cluster in B. subtilis with high editing efficiency, such as sacA, ganA, ligD & ligV, and bac operon. Especially, an extremely large gene cluster of 38 kb in B. subtilis genome was accurately deleted from the genome without introducing any unexpected mutations. Meanwhile, the synthetic platform was further upgraded to a version for multiplex genome editing, upon which two genes sacA and aprE were precisely and efficiently deleted using only one plasmid harboring two targeting sequences. In addition, we successfully inserted foreign genes into the genome of the chassis using the CRISPR-Cpf1 platform. Our work highlighted the availability of CRISPR-Cpf1 to gene manipulation in B. subtilis, including the flexible deletion of a single gene and multiple genes or a gene cluster, and gene knock-in. The designed genome-editing platform was easily and broadly applicable to other microorganisms. The novel platforms we constructed in this study provide a promising tool for efficient genome editing in diverse bacteria.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiao Lin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiaoqing Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangnan University (Rugao) Food Biotechnology Research Institute, Jiangsu, China
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