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Dong L, Manghwar H. Genome-wide expression analysis of LBD genes in tomato ( Solanum lycopersicum L.) under different light conditions. Plant Signal Behav 2023; 18:2290414. [PMID: 38059488 PMCID: PMC10732681 DOI: 10.1080/15592324.2023.2290414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Lateral organ boundaries (LOB) domain (LBD) genes, a gene family that encodes the transcription factors (TFs) of plants, plays crucial functions in the development and growth of plants. Currently, genome-wide studies of the LBD family are still limited to tomato (Solanum lycopersicum L.), which is considered an important economic crop. In this study, we performed a genome-wide analysis of LBD in tomato. In total, 56 LBDs were found in the tomato genome. Protein alignment and phylogenetic classification showed that LBDs were conserved with other species. Since light emitting diodes (LEDs) light have promising applications for tomato growth. To better understand the potential function of LBDs in response to LED light in tomato, we conducted a genome-wide expression analysis of LBD genes under different light conditions. As expected, different LED lights affected the tomato growth (e.g. hypocotyl length). RNA-seq data showed that eight LBDs in tomato seedlings were differentially expressed under different light treatments, including white, blue, red, and far-red light, compared to the dark-grown condition. It indicates that these LBDs might regulate plant development in different LED light conditions. Interestingly, two LBD genes (SlLBD1 and SlLBD2) were found to be differentially expressed in four distinct lights, which might be involved in regulating the plant architecture via a complicated TF network, which can be taken into consideration in further investigation.
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Affiliation(s)
- Limei Dong
- Guangdong Eco-engineering Polytechnic, Guangzhou, Guangdong, P.R. China
| | - Hakim Manghwar
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, Jiangxi, P.R. China
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Khoso MA, Zhang H, Khoso MH, Poudel TR, Wagan S, Papiashvili T, Saha S, Ali A, Murtaza G, Manghwar H, Liu F. Synergism of vesicle trafficking and cytoskeleton during regulation of plant growth and development: A mechanistic outlook. Heliyon 2023; 9:e21976. [PMID: 38034654 PMCID: PMC10682163 DOI: 10.1016/j.heliyon.2023.e21976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
The cytoskeleton is a fundamental component found in all eukaryotic organisms, serving as a critical factor in various essential cyto-biological mechanisms, particularly in the locomotion and morphological transformations of plant cells. The cytoskeleton is comprised of three main components: microtubules (MT), microfilaments (MF), and intermediate filaments (IF). The cytoskeleton plays a crucial role in the process of cell wall formation and remodeling throughout the growth and development of cells. It is a highly organized and regulated network composed of filamentous components. In the basic processes of intracellular transport, such as mitosis, cytokinesis, and cell polarity, the plant cytoskeleton plays a crucial role according to recent studies. The major flaws in the organization of the cytoskeletal framework are at the root of the aberrant organogenesis currently observed in plant mutants. The regulation of protein compartmentalization and abundance within cells is predominantly governed by the process of vesicle/membrane transport, which plays a crucial role in several signaling cascades.The regulation of membrane transport in eukaryotic cells is governed by a diverse array of proteins. Recent developments in genomics have provided new tools to study the evolutionary relationships between membrane proteins in different plant species. It is known that members of the GTPases, COP, SNAREs, Rabs, tethering factors, and PIN families play essential roles in vesicle transport between plant, animal, and microbial species. This Review presents the latest research on the plant cytoskeleton, focusing on recent developments related to the cytoskeleton and summarizing the role of various proteins in vesicle transport. In addition, the report predicts future research direction of plant cytoskeleton and vesicle trafficking, potential research priorities, and provides researchers with specific pointers to further investigate the significant link between cytoskeleton and vesicle trafficking.
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Affiliation(s)
- Muneer Ahmed Khoso
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Department of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Hailong Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Department of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Mir Hassan Khoso
- Department of Biochemistry, Shaheed Mohtarma Benazir Bhutto Medical University Larkana, Pakistan
| | - Tika Ram Poudel
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sindho Wagan
- Laboratory of Pest Physiology Biochemistry and Molecular Toxicology Department of Forest Protection Northeast Forestry University Harbin 150040, China
| | - Tamar Papiashvili
- School of Economics and Management Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Sudipta Saha
- School of Forestry, Department of Silviculture, Northeast Forestry University, Harbin 150040, China
| | - Abid Ali
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Department of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ghulam Murtaza
- Department of Biochemistry and Molecular Biology Harbin Medical University China, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
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Alam I, Zhang H, Du H, Rehman NU, Manghwar H, Lei X, Batool K, Ge L. Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production. J Agric Food Chem 2023; 71:3921-3938. [PMID: 36842151 DOI: 10.1021/acs.jafc.2c08051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.
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Affiliation(s)
- Intikhab Alam
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hanyin Zhang
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Huan Du
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Naveed Ur Rehman
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, SCAU, Guangzhou 510642, China
| | - Xiao Lei
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Khadija Batool
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
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Zhang J, Wu P, Li N, Xu X, Wang S, Chang S, Zhang Y, Wang X, Liu W, Ma Y, Manghwar H, Zhang X, Min L, Guo X. A male-sterile mutant with necrosis-like dark spots on anthers was generated in cotton. Front Plant Sci 2023; 13:1102196. [PMID: 36699851 PMCID: PMC9868585 DOI: 10.3389/fpls.2022.1102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Although conventional hybrid breeding has paved the way for improving cotton production and other properties, it is undoubtedly time and labor consuming, while the cultivation of male sterile line can fix the problem. Here, we induced male sterile mutants by simultaneously editing three cotton EXCESS MICROSPOROCYTES1 (GhEMS1) genes by CRISPR/Cas9. Notably, the GhEMS1 genes are homologous to AtEMS1 genes, which inhibit the production of middle layer and tapetum cells as well, leading to male sterility in cotton. Interestingly, there are necrosis-like dark spots on the surface of the anthers of GhEMS1s mutants, which is different from AtEMS1 mutant whose anther surface is clean and smooth, suggesting that the function of EMS1 gene has not been uncovered yet. Moreover, we have detected mutations in GhEMS1 genes from T0 to T3 mutant plants, which had necrosis-like dark spots as well, indicating that the mutation of the three GhEMS1 genes could be stably inherited. Dynamic transcriptomes showed plant hormone pathway and anther development genetic network were differential expression in mutant and wild-type anthers. And the lower level of IAA content in the mutant anthers than that in the wild type at four anther developmental stages may be the reason for the male sterility. This study not only facilitates the exploration of the basic research of cotton male sterile lines, but also provides germplasms for accelerating the hybrid breeding in cotton.
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Affiliation(s)
- Jun Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Peng Wu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ning Li
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaolan Xu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Songxin Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Siyuan Chang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuping Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xingxing Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wangshu Liu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xianlong Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaoping Guo
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Islam MAU, Nupur JA, Khalid MHB, Din AMU, Shafiq M, Alshegaihi RM, Ali Q, Ali Q, Kamran Z, Manzoor M, Haider MS, Shahid MA, Manghwar H. Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes (Basel) 2022; 13:2112. [PMID: 36421787 PMCID: PMC9690586 DOI: 10.3390/genes13112112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 10/13/2023] Open
Abstract
Zinc finger-homeodomain proteins are amongst the most prominent transcription factors (TFs) involved in biological processes, such as growth, development, and morphogenesis, and assist plants in alleviating the adverse effects of abiotic and biotic stresses. In the present study, genome-wide identification and expression analyses of the maize ZHD gene family were conducted. A total of 21 ZHD genes with different physicochemical properties were found distributed on nine chromosomes in maize. Through sequence alignment and phylogenetic analysis, we divided ZHD proteins into eight groups that have variations in gene structure, motif distribution, and a conserved ZF domain. Synteny analysis indicated duplication in four pairs of genes and the presence of orthologues of maize in monocots. Ka/Ks ratios suggested that strong pure selection occurred during evolution. Expression profiling revealed that the genes are evenly expressed in different tissues. Most of the genes were found to make a contribution to abiotic stress response, plant growth, and development. Overall, the evolutionary research on exons and introns, motif distributions, and cis-acting regions suggests that these genes play distinct roles in biological processes which may provide a basis for further study of these genes' functions in other crops.
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Affiliation(s)
- Md. Abir Ul Islam
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Juthy Abedin Nupur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Muhammad Hayder Bin Khalid
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Atta Mohi Ud Din
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Key Laboratory of Crop Physiology Ecology and Production Management, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Muhammad Shafiq
- Department of Horticulture, University of the Punjab, Lahore 54000, Pakistan
| | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Qurban Ali
- Department of Plant Breeding and Genetics, University of the Punjab, Lahore 54000, Pakistan
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zuha Kamran
- Department of Horticulture, University of the Punjab, Lahore 54000, Pakistan
| | - Mujahid Manzoor
- Department of Entomology, University of the Punjab, Lahore 54000, Pakistan
| | | | - Muhammad Adnan Shahid
- Horticultural Sciences Department, University of Florida/IFAS, North Florida Research and Education Center, Quincy, FL 32351, USA
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
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Alam I, Manghwar H, Zhang H, Yu Q, Ge L. Identification of GOLDEN2-like transcription factor genes in soybeans and their role in regulating plant development and metal ion stresses. Front Plant Sci 2022; 13:1052659. [PMID: 36438095 PMCID: PMC9691782 DOI: 10.3389/fpls.2022.1052659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The Golden 2-Like (G2-like or GLK) transcription factors are essential for plant growth, development, and many stress responses as well as heavy metal stress. However, G2-like regulatory genes have not been studied in soybean. This study identified the genes for 130 G2-Like candidates' in the genome of Glycine max (soybean). These GLK genes were located on all 20 chromosomes, and several of them were segmentally duplicated. Most GLK family proteins are highly conserved in Arabidopsis and soybean and were classified into five major groups based on phylogenetic analysis. These GmGLK gene promoters share cis-acting elements involved in plant responses to abscisic acid, methyl jasmonate, auxin signaling, low temperature, and biotic and abiotic stresses. RNA-seq expression data revealed that the GLK genes were classified into 12 major groups and differentially expressed in different tissues or organs. The co-expression network complex revealed that the GmGLK genes encode proteins involved in the interaction of genes related to chlorophyll biosynthesis, circadian rhythms, and flowering regulation. Real-time quantitative PCR analysis confirmed the expression profiles of eight GLK genes in response to cadmium (Cd) and copper (Cu) stress, with some GLK genes significantly induced by both Cd and Cu stress treatments, implying a functional role in defense responsiveness. Thus, we present a comprehensive perspective of the GLK genes in soybean and emphasize their important role in crop development and metal ion stresses.
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Affiliation(s)
- Intikhab Alam
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- College of Life Sciences, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Hanyin Zhang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Qianxia Yu
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
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Khoso MA, Hussain A, Ritonga FN, Ali Q, Channa MM, Alshegaihi RM, Meng Q, Ali M, Zaman W, Brohi RD, Liu F, Manghwar H. WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants. Front Plant Sci 2022; 13:1039329. [PMID: 36426143 PMCID: PMC9679293 DOI: 10.3389/fpls.2022.1039329] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 06/01/2023]
Abstract
The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.
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Affiliation(s)
- Muneer Ahmed Khoso
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- Department of Life Science, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Amjad Hussain
- College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | | | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Qinglin Meng
- Department of Biology and Food Engineering, Bozhou University, Bozhou, China
| | - Musrat Ali
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad Pakistan, Islamabad, Pakistan
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Rahim Dad Brohi
- Department of Animal Reproduction/Theriogenology, Faculty of Veterinary Science, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
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Ayaz M, Ali Q, Jiang Q, Wang R, Wang Z, Mu G, Khan SA, Khan AR, Manghwar H, Wu H, Gao X, Gu Q. Salt Tolerant Bacillus Strains Improve Plant Growth Traits and Regulation of Phytohormones in Wheat under Salinity Stress. Plants (Basel) 2022; 11:plants11202769. [PMID: 36297795 PMCID: PMC9608499 DOI: 10.3390/plants11202769] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 05/30/2023]
Abstract
Soil salinity is a major constraint adversely affecting agricultural crops including wheat worldwide. The use of plant growth promoting rhizobacteria (PGPR) to alleviate salt stress in crops has attracted the focus of many researchers due to its safe and eco-friendly nature. The current study aimed to study the genetic potential of high halophilic Bacillus strains, isolated from the rhizosphere in the extreme environment of the Qinghai-Tibetan plateau region of China, to reduce salt stress in wheat plants. The genetic analysis of high halophilic strains, NMCN1, LLCG23, and moderate halophilic stain, FZB42, revealed their key genetic features that play an important role in salt stress, osmotic regulation, signal transduction and membrane transport. Consequently, the expression of predicted salt stress-related genes were upregulated in the halophilic strains upon NaCl treatments 10, 16 and 18%, as compared with control. The halophilic strains also induced a stress response in wheat plants through the regulation of lipid peroxidation, abscisic acid and proline in a very efficient manner. Furthermore, NMCN1 and LLCG23 significantly enhanced wheat growth parameters in terms of physiological traits, i.e., fresh weight 31.2% and 29.7%, dry weight 28.6% and 27.3%, shoot length 34.2% and 31.3% and root length 32.4% and 30.2%, respectively, as compared to control plants under high NaCl concentration (200 mmol). The Bacillus strains NMCN1 and LLCG23 efficiently modulated phytohormones, leading to the substantial enhancement of plant tolerance towards salt stress. Therefore, we concluded that NMCN1 and LLCG23 contain a plethora of genetic features enabling them to combat with salt stress, which could be widely used in different bio-formulations to obtain high crop production in saline conditions.
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Affiliation(s)
- Muhammad Ayaz
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifan Jiang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruoyi Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqi Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangyuan Mu
- Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen 518057, China
| | - Sabaz Ali Khan
- Biotechnology Department, College of Environmental Sciences, COMSATS, Abbottabad 22060, Pakistan
| | - Abdur Rashid Khan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qin Gu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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9
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Liang Z, Ali Q, Wang Y, Mu G, Kan X, Ren Y, Manghwar H, Gu Q, Wu H, Gao X. Toxicity of Bacillus thuringiensis Strains Derived from the Novel Crystal Protein Cry31Aa with High Nematicidal Activity against Rice Parasitic Nematode Aphelenchoides besseyi. Int J Mol Sci 2022; 23:ijms23158189. [PMID: 35897765 PMCID: PMC9331774 DOI: 10.3390/ijms23158189] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
The plant parasitic nematode, Aphelenchoides besseyi, is a serious pest causing severe damage to various crop plants and vegetables. The Bacillus thuringiensis (Bt) strains, GBAC46 and NMTD81, and the biological strain, FZB42, showed higher nematicidal activity against A. besseyi, by up to 88.80, 82.65, and 75.87%, respectively, in a 96-well plate experiment. We screened the whole genomes of the selected strains by protein-nucleic acid alignment. It was found that the Bt strain GBAC46 showed three novel crystal proteins, namely, Cry31Aa, Cry73Aa, and Cry40ORF, which likely provide for the safe control of nematodes. The Cry31Aa protein was composed of 802 amino acids with a molecular weight of 90.257 kDa and contained a conserved delta-endotoxin insecticidal domain. The Cry31Aa exhibited significant nematicidal activity against A. besseyi with a lethal concentration (LC50) value of 131.80 μg/mL. Furthermore, the results of in vitro experiments (i.e., rhodamine and propidium iodide (PI) experiments) revealed that the Cry31Aa protein was taken up by A. besseyi, which caused damage to the nematode's intestinal cell membrane, indicating that the Cry31Aa produced a pore-formation toxin. In pot experiments, the selected strains GBAC46, NMTD81, and FZB42 significantly reduced the lesions on leaves by up to 33.56%, 45.66, and 30.34% and also enhanced physiological growth parameters such as root length (65.10, 50.65, and 55.60%), shoot length (68.10, 55.60, and 59.45%), and plant fresh weight (60.71, 56.45, and 55.65%), respectively. The number of nematodes obtained from the plants treated with the selected strains (i.e., GBAC46, NMTD81, and FZB42) and A. besseyi was significantly reduced, with 0.56, 0.83., 1.11, and 5.04 seedling mL-1 nematodes were achieved, respectively. Moreover, the qRT-PCR analysis showed that the defense-related genes were upregulated, and the activity of hydrogen peroxide (H2O2) increased while malondialdehyde (MDA) decreased in rice leaves compared to the control. Therefore, it was concluded that the Bt strains GBAC46 and NMTD81 can promote rice growth, induce high expression of rice defense-related genes, and activate systemic resistance in rice. More importantly, the application of the novel Cry31Aa protein has high potential for the efficient and safe prevention and green control of plant parasitic nematodes.
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Affiliation(s)
- Zhao Liang
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qurban Ali
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Wang
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangyuan Mu
- Shenzhen Batian Ecotypic Engineering Co., Ltd., Shenzhen 518057, China; (G.M.); (X.K.)
| | - Xuefei Kan
- Shenzhen Batian Ecotypic Engineering Co., Ltd., Shenzhen 518057, China; (G.M.); (X.K.)
| | - Yajun Ren
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China;
| | - Qin Gu
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Huijun Wu
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuewen Gao
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, China; (Z.L.); (Q.A.); (Y.W.); (Y.R.); (Q.G.); (H.W.)
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: ; Tel.: +86-025-8439-5268
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10
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Cheng S, Wang Q, Manghwar H, Liu F. Autophagy-Mediated Regulation of Different Meristems in Plants. Int J Mol Sci 2022; 23:ijms23116236. [PMID: 35682913 PMCID: PMC9180974 DOI: 10.3390/ijms23116236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a highly conserved cell degradation process that widely exists in eukaryotic cells. In plants, autophagy helps maintain cellular homeostasis by degrading and recovering intracellular substances through strict regulatory pathways, thus helping plants respond to a variety of developmental and environmental signals. Autophagy is involved in plant growth and development, including leaf starch degradation, senescence, anthers development, regulation of lipid metabolism, and maintenance of peroxisome mass. More and more studies have shown that autophagy plays a role in stress response and contributes to maintain plant survival. The meristem is the basis for the formation and development of new tissues and organs during the post-embryonic development of plants. The differentiation process of meristems is an extremely complex process, involving a large number of morphological and structural changes, environmental factors, endogenous hormones, and molecular regulatory mechanisms. Recent studies have demonstrated that autophagy relates to meristem development, affecting plant growth and development under stress conditions, especially in shoot and root apical meristem. Here, we provide an overview of the current knowledge about how autophagy regulates different meristems under different stress conditions and possibly provide new insights for future research.
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Affiliation(s)
| | | | | | - Fen Liu
- Correspondence: (H.M.); (F.L.)
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11
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Ali Q, Zheng H, Rao MJ, Ali M, Hussain A, Saleem MH, Nehela Y, Sohail MA, Ahmed AM, Kubar KA, Ali S, Usman K, Manghwar H, Zhou L. Advances, limitations, and prospects of biosensing technology for detecting phytopathogenic bacteria. Chemosphere 2022; 296:133773. [PMID: 35114264 DOI: 10.1016/j.chemosphere.2022.133773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 05/22/2023]
Abstract
Phytopathogenic bacteria cause severe economic losses in agricultural production worldwide. The spread rates, severity, and emerging plant bacterial diseases have become serious threat to the sustainability of food sources and the fruit industry. Detection and diagnosis of plant diseases are imperative in order to manage plant diseases in field conditions, greenhouses, and food storage conditions as well as to maximize agricultural productivity and sustainability. To date, various techniques including, serological, observation-based, and molecular methods have been employed for plant disease detection. These methods are sensitive and specific for genetic identification of bacteria. However, these methods are specific for genetic identification of bacteria. Currently, the innovative biosensor-based disease detection technique is an attractive and promising alternative. A biosensor system involves biological recognition and transducer active receptors based on sensors used in plant-bacteria diagnosis. This system has been broadly used for the rapid diagnosis of plant bacterial pathogens. In the present review, we have discussed the conventional methods of bacterial-disease detection, however, the present review mainly focuses on the applications of different biosensor-based techniques along with point-of-care (POC), robotics, and cell phone-based systems. In addition, we have also discussed the challenges and limitations of these techniques.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, 210095, China.
| | - Hongxia Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Muhammad Junaid Rao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, PR China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yasser Nehela
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Rd, Lake Alfred, FL, 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Agha Mushtaque Ahmed
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University Tando Jam, Sindh, Pakistan
| | - Kashif Ali Kubar
- Faculty of Agriculture, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, 90150, Balochistan, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Allama Iqbal Road, 38000, Faisalabad, Pakistan
| | - Kamal Usman
- Agricultural Research Station, Office of VP for Research & Graduate Studies, Qatar University, 2713, Doha, Qatar
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China.
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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12
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Meng Q, Manghwar H, Hu W. Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization. Plants (Basel) 2022; 11:1211. [PMID: 35567211 PMCID: PMC9102695 DOI: 10.3390/plants11091211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.
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Affiliation(s)
- Qinglin Meng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Weiming Hu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
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13
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. Front Plant Sci 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Ali Q, Ayaz M, Mu G, Hussain A, Yuanyuan Q, Yu C, Xu Y, Manghwar H, Gu Q, Wu H, Gao X. Revealing plant growth-promoting mechanisms of Bacillus strains in elevating rice growth and its interaction with salt stress. Front Plant Sci 2022; 13:994902. [PMID: 36119605 PMCID: PMC9479341 DOI: 10.3389/fpls.2022.994902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/10/2022] [Indexed: 05/04/2023]
Abstract
Soil salinity is a major environmental stress that has been negatively affecting the growth and productivity of rice. However, various salt-resistant plant growth-promoting rhizobacteria (PGPR) have been known to promote plant growth and alleviate the damaging effects of salt stress via mitigating physio-biochemical and molecular characteristics. This study was conducted to examine the salt stress potential of Bacillus strains identified from harsh environments of the Qinghai-Tibetan plateau region of China. The Bacillus strains NMTD17, GBSW22, and FZB42 were screened for their response under different salt stress conditions (1, 4, 7, 9, 11, 13, and 16%). The screening analysis revealed strains NMTD17, GBSW22, and FZB42 to be high-salt tolerant, moderate-salt tolerant, and salt-sensitive, respectively. The NMTD17 strain produced a strong biofilm, followed by GBSW22 and FZB42. The expression of salt stress-related genes in selected strains was also analyzed through qPCR in various salt concentrations. Further, the Bacillus strains were used in pot experiments to study their growth-promoting ability and antioxidant activities at various concentrations (0, 100, 150, and 200 mmol). The analysis of growth-promoting traits in rice exhibited that NMTD17 had a highly significant effect and GSBW22 had a moderately significant effect in comparison with FZB42. The highly resistant strain NMTD17 that stably promoted rice plant growth was further examined for its function in the composition of rhizobacterial communities. The inoculation of NMTD17 increased the relative abundance and richness of rhizobacterial species. These outcomes propose that NMTD17 possesses the potential of PGPR traits, antioxidants enzyme activities, and reshaping the rhizobacterial community that together mitigate the harmful effects of salinity in rice plants.
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Affiliation(s)
- Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Ayaz
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Guangyuan Mu
- Shenzhen Batian Ecotypic Engineering Co., Ltd., Shenzhen, China
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qiu Yuanyuan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Yujiao Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Qin Gu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Huijun Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
| | - Xuewen Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, The Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Xuewen Gao,
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15
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Hussain A, Ding X, Alariqi M, Manghwar H, Hui F, Li Y, Cheng J, Wu C, Cao J, Jin S. Herbicide Resistance: Another Hot Agronomic Trait for Plant Genome Editing. Plants (Basel) 2021; 10:621. [PMID: 33805182 PMCID: PMC8064318 DOI: 10.3390/plants10040621] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Abstract
Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a rapidly increasing human population. Chemical weed control (herbicides) along with integrated weed management (IWM) practices can be the most effective and reliable method of weed management programs. The application of herbicides for weed control practices calls for the urgency to develop herbicide-resistant (HR) crops. Recently, genome editing tools, especially CRISPR-Cas9, have brought innovation in genome editing technology that opens up new possibilities to provide sustainable farming in modern agricultural industry. To date, several non-genetically modified (GM) HR crops have been developed through genome editing that can present a leading role to combat weed problems along with increasing crop productivity to meet increasing food demand around the world. Here, we present the chemical method of weed control, approaches for herbicide resistance development, and possible advantages and limitations of genome editing in herbicide resistance. We also discuss how genome editing would be effective in combating intensive weed problems and what would be the impact of genome-edited HR crops in agriculture.
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Affiliation(s)
- Amjad Hussain
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Xiao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Hakim Manghwar
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
| | - Fengjiao Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Yapei Li
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Junqi Cheng
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Chenglin Wu
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Jinlin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
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16
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Khan AH, Min L, Ma Y, Wu Y, Ding Y, Li Y, Xie S, Ullah A, Shaban M, Manghwar H, Shahid M, Zhao Y, Wang C, Zhang X. High day and night temperatures distinctively disrupt fatty acid and jasmonic acid metabolism, inducing male sterility in cotton. J Exp Bot 2020; 71:6128-6141. [PMID: 32640017 DOI: 10.1093/jxb/eraa319] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
High temperature stress is an inevitable environmental factor in certain geographical regions. To study the effect of day and night high temperature stress on male reproduction, the heat-sensitive cotton line H05 was subjected to high temperature stress. High day/normal night (HN) and normal day/high night (NH) temperature treatments were compared with normal day/normal night (NN) temperature as a control. At the anther dehiscence stage, significant differences were observed, with a reduction in flower size and filament length, and sterility in pollen, seen in NH more than in HN. A total of 36 806 differentially expressed genes were screened, which were mainly associated with fatty acid and jasmonic acid (JA) metabolic pathways. Fatty acid and JA contents were reduced more in NH than HN. Under NH, ACYL-COA OXIDASE 2 (ACO2), a JA biosynthesis gene, was down-regulated. Interestingly, aco2 CRISPR-Cas9 mutants showed male sterility under the NN condition. The exogenous application of methyl jasmonate to early-stage buds of mutants rescued the sterile pollen and indehiscent anther phenotypes at the late stage. These data show that high temperature at night may affect fatty acid and JA metabolism in anthers by suppressing GhACO2 and generate male sterility more strongly than high day temperature.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sai Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Botany, University of Malakand, Dir Lower, Khyber Pakhtunkwa, Pakistan
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Shahid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yunlong Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaozhi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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17
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Zhang D, Hussain A, Manghwar H, Xie K, Xie S, Zhao S, Larkin RM, Qing P, Jin S, Ding F. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. Plant Biotechnol J 2020; 18:1651-1669. [PMID: 32271968 PMCID: PMC7336378 DOI: 10.1111/pbi.13383] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/22/2020] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR-Cas system, has led to significant progress in the field of plant and animal breeding. The CRISPR-Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter diverse genomes (e.g. genomes from both plants and animals) including human genomes with unprecedented ease, accuracy and high efficiency. The recent development and scope of CRISPR-Cas system have raised new regulatory challenges around the world due to moral, ethical, safety and technical concerns associated with its applications in pre-clinical and clinical research, biomedicine and agriculture. Here, we review the art, applications and potential risks of CRISPR-Cas system in genome editing. We also highlight the patent and ethical issues of this technology along with regulatory frameworks established by various nations to regulate CRISPR-Cas-modified organisms/products.
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Affiliation(s)
- Debin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kabin Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ping Qing
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fang Ding
- Hubei Key Laboratory of Plant PathologyCollege of Plant Sciences and TechnologyHuazhong Agricultural UniversityWuhanChina
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18
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Manghwar H, Li B, Ding X, Hussain A, Lindsey K, Zhang X, Jin S. CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off-Target Evaluation, and Strategies to Mitigate Off-Target Effects. Adv Sci (Weinh) 2020; 7:1902312. [PMID: 32195078 PMCID: PMC7080517 DOI: 10.1002/advs.201902312] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/07/2019] [Indexed: 05/03/2023]
Abstract
Life sciences have been revolutionized by genome editing (GE) tools, including zinc finger nucleases, transcription activator-Like effector nucleases, and CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas (CRISPR-associated) systems, which make the targeted modification of genomic DNA of all organisms possible. CRISPR/Cas systems are being widely used because of their accuracy, efficiency, and cost-effectiveness. Various classes of CRISPR/Cas systems have been developed, but their extensive use may be hindered by off-target effects. Efforts are being made to reduce the off-target effects of CRISPR/Cas9 by generating various CRISPR/Cas systems with high fidelity and accuracy. Several approaches have been applied to detect and evaluate the off-target effects. Here, the current GE tools, the off-target effects generated by GE technology, types of off-target effects, mechanisms of off-target effects, major concerns, and outcomes of off-target effects in plants and animals are summarized. The methods to detect off-target effects, tools for single-guide RNA (sgRNA) design, evaluation and prediction of off-target effects, and strategies to increase the on-target efficiency and mitigate the off-target impact on intended genome-editing outcomes are summarized.
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Affiliation(s)
- Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Bo Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
- Institute of Nuclear and Biological TechnologiesXinjiang Academy of Agricultural SciencesUrumqiXinjiang830091P. R. China
| | - Xiao Ding
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversityDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070P. R. China
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19
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Qin L, Li J, Wang Q, Xu Z, Sun L, Alariqi M, Manghwar H, Wang G, Li B, Ding X, Rui H, Huang H, Lu T, Lindsey K, Daniell H, Zhang X, Jin S. High-efficient and precise base editing of C•G to T•A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system. Plant Biotechnol J 2020; 18:45-56. [PMID: 31116473 PMCID: PMC6920158 DOI: 10.1111/pbi.13168] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The base-editing technique using CRISPR/nCas9 (Cas9 nickase) or dCas9 (deactivated Cas9) fused with cytidine deaminase is a powerful tool to create point mutations. In this study, a novel G. hirsutum-Base Editor 3 (GhBE3) base-editing system has been developed to create single-base mutations in the allotetraploid genome of cotton (Gossypium hirsutum). A cytidine deaminase sequence (APOBEC) fused with nCas9 and uracil glycosylase inhibitor (UGI) was inserted into our CRISPR/Cas9 plasmid (pRGEB32-GhU6.7). Three target sites were chosen for two target genes, GhCLA and GhPEBP, to test the efficiency and accuracy of GhBE3. The editing efficiency ranged from 26.67 to 57.78% at the three target sites. Targeted deep sequencing revealed that the C→T substitution efficiency within an 'editing window', approximately six-nucleotide windows of -17 to -12 bp from the PAM sequence, was up to 18.63% of the total sequences. The 27 most likely off-target sites predicted by CRISPR-P and Cas-OFFinder tools were analysed by targeted deep sequencing, and it was found that rare C→T substitutions (average < 0.1%) were detected in the editing windows of these sites. Furthermore, whole-genome sequencing analyses on two GhCLA-edited and one wild-type plants with about 100× depth showed that no bona fide off-target mutations were detectable from 1500 predicted potential off-target sites across the genome. In addition, the edited bases were inherited to T1 progeny. These results demonstrate that GhBE3 has high specificity and accuracy for the generation of targeted point mutations in allotetraploid cotton.
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Affiliation(s)
- Lei Qin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jianying Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qiongqiong Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhongping Xu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lin Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guanyin Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Bo Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiao Ding
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hangping Rui
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Huimei Huang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Tianliang Lu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | | | - Henry Daniell
- Department of BiochemistrySchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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20
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Manghwar H, Lindsey K, Zhang X, Jin S. CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. Trends Plant Sci 2019; 24:1102-1125. [PMID: 31727474 DOI: 10.1016/j.tplants.2019.09.006] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 05/20/2023]
Abstract
Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.
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Affiliation(s)
- Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
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21
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Li J, Manghwar H, Sun L, Wang P, Wang G, Sheng H, Zhang J, Liu H, Qin L, Rui H, Li B, Lindsey K, Daniell H, Jin S, Zhang X. Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants. Plant Biotechnol J 2019; 17:858-868. [PMID: 30291759 PMCID: PMC6587709 DOI: 10.1111/pbi.13020] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 05/19/2023]
Abstract
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and three negative (Ne) control and three wild-type (WT) plants. In total, 4188-6404 unique single-nucleotide polymorphisms (SNPs) and 312-745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared to WT, negative and cotton reference genome sequences. Since the majority of these variations lack a protospacer-adjacent motif (PAM), we demonstrated that the most variations following Cas9-edited are due either to somaclonal variation or/and pre-existing/inherent variation from maternal plants, but not off-target effects. Of a total of 4413 potential off-target sites (allowing ≤5 mismatches within the 20-bp sgRNA and 3-bp PAM sequences), the WGS data revealed that only four are bona fide off-target indel mutations, validated by Sanger sequencing. Moreover, inherent genetic variation of WT can generate novel off-target sites and destroy PAMs, which suggested great care should be taken to design sgRNA for the minimizing of off-target effect. These findings suggested that CRISPR/Cas9 system is highly specific for cotton plants.
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Affiliation(s)
- Jianying Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lin Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hanyan Sheng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jie Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hao Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Agricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of InformaticsHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lei Qin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hangping Rui
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Bo Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | | | - Henry Daniell
- Department of BiochemistrySchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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22
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Ullah A, Akbar A, Luo Q, Khan AH, Manghwar H, Shaban M, Yang X. Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions. Microb Ecol 2019; 77:429-439. [PMID: 30196314 DOI: 10.1007/s00248-018-1260-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/02/2018] [Indexed: 05/18/2023]
Abstract
Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Adnan Akbar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Qingqing Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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23
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Ullah A, Manghwar H, Shaban M, Khan AH, Akbar A, Ali U, Ali E, Fahad S. Phytohormones enhanced drought tolerance in plants: a coping strategy. Environ Sci Pollut Res Int 2018; 25:33103-33118. [PMID: 30284160 DOI: 10.1007/s11356-018-3364-5] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/27/2018] [Indexed: 05/20/2023]
Abstract
Drought stress is a severe environmental constraint among the emerging problems. Plants are highly vulnerable to drought stress and a severe decrease in yield was recorded in the last few decades. So, it is highly desirable to understand the mechanism of drought tolerance in plants and consequently enhance the tolerance against drought stress. Phytohormones are known to play vital roles in regulating various phenomenons in plants to acclimatize to varying drought environment. Abscisic acid (ABA) is considered the main hormone which intensifies drought tolerance in plants through various morpho-physiological and molecular processes including stomata regulation, root development, and initiation of ABA-dependent pathway. In addition, jasmonic acid (JA), salicylic acid (SA) ethylene (ET), auxins (IAA), gibberellins (GAs), cytokinins (CKs), and brassinosteroids (BRs) are also very important phytohormones to congregate the challenges of drought stress. However, these hormones are usually cross talk with each other to increase the survival of plants in drought conditions. On the other hand, the transgenic approach is currently the most accepted technique to engineer the genes responsible for the synthesis of phytohormones in drought stress response. Our present review highlights the regulatory circuits of phytohormones in drought tolerance mechanism.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- Department of Botany, University of Malakand, Chakdara Dir Lower, Khyber Pakhtunkhwa, 18550, Pakistan.
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Adnan Akbar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Usman Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Ehsan Ali
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shah Fahad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Department of Agriculture, University of Swabi, Swabi, KPK, Pakistan
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