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Motoche-Monar C, Ordoñez JE, Chang O, Gonzales-Zubiate FA. gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement. Biomolecules 2023; 13:1698. [PMID: 38136570 PMCID: PMC10741458 DOI: 10.3390/biom13121698] [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: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 12/24/2023] Open
Abstract
Over the past decade, genetic engineering has witnessed a revolution with the emergence of a relatively new genetic editing tool based on RNA-guided nucleases: the CRISPR/Cas9 system. Since the first report in 1987 and characterization in 2007 as a bacterial defense mechanism, this system has garnered immense interest and research attention. CRISPR systems provide immunity to bacteria against invading genetic material; however, with specific modifications in sequence and structure, it becomes a precise editing system capable of modifying the genomes of a wide range of organisms. The refinement of these modifications encompasses diverse approaches, including the development of more accurate nucleases, understanding of the cellular context and epigenetic conditions, and the re-designing guide RNAs (gRNAs). Considering the critical importance of the correct performance of CRISPR/Cas9 systems, our scope will emphasize the latter approach. Hence, we present an overview of the past and the most recent guide RNA web-based design tools, highlighting the evolution of their computational architecture and gRNA characteristics over the years. Our study explains computational approaches that use machine learning techniques, neural networks, and gRNA/target interactions data to enable predictions and classifications. This review could open the door to a dynamic community that uses up-to-date algorithms to optimize and create promising gRNAs, suitable for modern CRISPR/Cas9 engineering.
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Affiliation(s)
- Cristofer Motoche-Monar
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Julián E. Ordoñez
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Oscar Chang
- Departamento de Electrónica, Universidad Simon Bolivar, Caracas 1080, Venezuela
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
| | - Fernando A. Gonzales-Zubiate
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
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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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3
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Umer MJ, Zheng J, Yang M, Batool R, Abro AA, Hou Y, Xu Y, Gebremeskel H, Wang Y, Zhou Z, Cai X, Liu F, Zhang B. Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer. Funct Integr Genomics 2023; 23:142. [PMID: 37121989 DOI: 10.1007/s10142-023-01065-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
The soil-borne pathogen Verticillium dahliae, also referred as "The Cotton Cancer," is responsible for causing Verticillium wilt in cotton crops, a destructive disease with a global impact. To infect cotton plants, the pathogen employs multiple virulence mechanisms such as releasing enzymes that degrade cell walls, activating genes that contribute to virulence, and using protein effectors. Conversely, cotton plants have developed numerous defense mechanisms to combat the impact of V. dahliae. These include strengthening the cell wall by producing lignin and depositing callose, discharging reactive oxygen species, and amassing hormones related to defense. Despite the efforts to develop resistant cultivars, there is still no permanent solution to Verticillium wilt due to a limited understanding of the underlying molecular mechanisms that drive both resistance and pathogenesis is currently prevalent. To address this challenge, cutting-edge technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), host-induced gene silencing (HIGS), and gene delivery via nano-carriers could be employed as effective alternatives to control the disease. This article intends to present an overview of V. dahliae virulence mechanisms and discuss the different cotton defense mechanisms against Verticillium wilt, including morphophysiological and biochemical responses and signaling pathways including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and strigolactones (SLs). Additionally, the article highlights the significance of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) in gene expression regulation, as well as the different methods employed to identify and functionally validate genes to achieve resistance against this disease. Gaining a more profound understanding of these mechanisms could potentially result in the creation of more efficient strategies for combating Verticillium wilt in cotton crops.
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Affiliation(s)
- Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
| | - Mengying Yang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Raufa Batool
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aamir Ali Abro
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haileslassie Gebremeskel
- Mehoni Agricultural Research Center, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.
| | - Baohong Zhang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Zhao Z, Qi Y, Yang Z, Cheng L, Sharif R, Raza A, Chen P, Hou D, Li Y. Exploring the Agrobacterium-mediated transformation with CRISPR/Cas9 in cucumber (Cucumis sativus L.). Mol Biol Rep 2022; 49:11481-11490. [PMID: 36057005 DOI: 10.1007/s11033-022-07558-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/03/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUNDS The narrow genetic basis of cucumber makes breeding of this species difficult. CRISPR/Cas9 system is characteristic of simple design, low cost and high efficiency, which has opened a new path for cucumber functional genetics and the development of cucumber mocular breeding. However, the immature genetic transformation system is the main limiting factor for applying this technology in cucumber. METHODS AND RESULTS In this study, a Histochemical β-glucuronidase (GUS) assay was used to analyze the effect of various parameters, including slight scratch of explants, pre-culture time, acetosyringone (AS) concentration, infection time in Agrobacterium solution, and co-culture period on the transformation efficiency. The results showed that the explants slightly scratched after cutting, pre-cultured for 1 day, Agrobacterium bacterial solution containing AS, and 20 min length of infection could significantly increase the GUS staining rate of explants. On this basis, two sequences with high specificity (sgRNA-1 and sgRNA-2) targeted different loci of gene CsGCN5 were designed. The corresponding vectors Cas9-sgRNA-1 and Cas9-sgRNA-2 were constructed and transformed using the above-optimized cucumber genetic transformation system, and three and two PCR positive lines were obtained from 210 and 207 explants, respectively. No sequence mutation at target loci of CsGCN5 was detected in the Cas9-sgRNA-1 transformed three PCR positive lines. However, one mutant line with targeted homozygous change was recognized from the Cas9-sgRNA-2 transformed two PCR positive lines. CONCLUSION In this study, 2.4‰ of total explants had directed mutation in the CsGCN5 gene. The results in the present study would be beneficial to further optimize and improve the efficiency of the genetic transformation of cucumber.
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Affiliation(s)
- Ziyao Zhao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yaguang Qi
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhimin Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Liyu Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dong Hou
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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CRISPR/Cas9-Mediated Mutagenesis of the Granule-Bound Starch Synthase Gene in the Potato Variety Yukon Gold to Obtain Amylose-Free Starch in Tubers. Int J Mol Sci 2022; 23:ijms23094640. [PMID: 35563030 PMCID: PMC9101600 DOI: 10.3390/ijms23094640] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
Potato (Solanum tuberosum L.) is the third most important food crop after rice and wheat. Its tubers are a rich source of dietary carbohydrates in the form of starch, which has many industrial applications. Starch is composed of two polysaccharides, amylose and amylopectin, and their ratios determine different properties and functionalities. Potato varieties with higher amylopectin have many food processing and industrial applications. Using Agrobacterium-mediated transformation, we delivered Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) reagents to potato (variety Yukon Gold) cells to disrupt the granule-bound starch synthase (gbssI) gene with the aim of eliminating the amylose component of starch. Lugol-Iodine staining of the tubers showed a reduction or complete elimination of amylose in some of the edited events. These results were further confirmed by the perchloric acid and enzymatic methods. One event (T2-7) showed mutations in all four gbss alleles and total elimination of amylose from the tubers. Viscosity profiles of the tuber starch from six different knockout events were determined using a Rapid Visco Analyzer (RVA), and the values reflected the amylopectin/amylose ratio. Follow-up studies will focus on eliminating the CRISPR components from the events and on evaluating the potential of clones with various amylose/amylopectin ratios for food processing and other industrial applications.
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Aslam S, Khan SH, Ahmad A, Walawage SL, Dandekar AM. Founder transformants of cotton (Gossypium hirsutum L.) obtained through the introduction of DS-Red, Rec, Rep and CRISPR/Cas9 expressing constructs for developing base lines of recombinase mediated gene stacking. PLoS One 2022; 17:e0263219. [PMID: 35113911 PMCID: PMC8812945 DOI: 10.1371/journal.pone.0263219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Cotton being the major fiber crop across the world is exposed to numerous biotic and abiotic stresses. Genetic transformation of cotton is vital to meet the world’s food, feed and fiber demands. Genetic manipulation by randomly transferring the genes emanate variable gene expression. Targeted gene insertion by latest genome editing tools results in predictable expression of genes at a specified location. Gene stacking technology emerged as an adaptive strategy to combat biotic and abiotic stresses by integrating 2–3 genes simultaneously and at a specific site to avoid variable gene expression at diverse locations. This study explains the development of cotton’s founder transformants to be used as a base line for multiple gene stacking projects. We introduced Cre and PhiC31 mediated recombination sites to specify the locus of incoming genes. CRISPR-Cas9 gene was integrated for developing CRISPR based founder lines of cotton. Cas9 gene along with gRNA was integrated to target Rep (replication) region of cotton leaf curl virus. Replication region of virus was specifically targeted to diminish further proliferation and preventing the virus to develop new strains. To successfully develop these primary transformants, a model transformation system has been optimized with the red color visualization (DS-Red). Following red color transformation system, three baselines with recombination specified site (Rec), targeted replication region (Rep) and Cas9 founder lines have been developed. These founder transformants are useful for developing recombinase mediated and CRISPR/Cas9 based originator lines of cotton. Moreover, these transformants will set up a base system for all the recombinase mediated gene stacking projects.
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Affiliation(s)
- Sabin Aslam
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- * E-mail: ,
| | - Sultan Habibullah Khan
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Sriema Lalani Walawage
- Department of Plant Sciences, School of Biological Sciences, University of California, Davis, California, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, School of Biological Sciences, University of California, Davis, California, United States of America
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7
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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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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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9
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Zhang Z, Li J, Jamshed M, Shi Y, Liu A, Gong J, Wang S, Zhang J, Sun F, Jia F, Ge Q, Fan L, Zhang Z, Pan J, Fan S, Wang Y, Lu Q, Liu R, Deng X, Zou X, Jiang X, Liu P, Li P, Iqbal MS, Zhang C, Zou J, Chen H, Tian Q, Jia X, Wang B, Ai N, Feng G, Wang Y, Hong M, Li S, Lian W, Wu B, Hua J, Zhang C, Huang J, Xu A, Shang H, Gong W, Yuan Y. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:239-253. [PMID: 31199554 PMCID: PMC6920336 DOI: 10.1111/pbi.13191] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/02/2023]
Abstract
Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.
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10
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Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R. Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells 2019; 8:E1386. [PMID: 31689989 PMCID: PMC6912757 DOI: 10.3390/cells8111386] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/04/2019] [Accepted: 10/12/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-editing, a recent technological advancement in the field of life sciences, is one of the great examples of techniques used to explore the understanding of the biological phenomenon. Besides having different site-directed nucleases for genome editing over a decade ago, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) based genome editing approach has become a choice of technique due to its simplicity, ease of access, cost, and flexibility. In the present review, several CRISPR/Cas based approaches have been discussed, considering recent advances and challenges to implicate those in the crop improvement programs. Successful examples where CRISPR/Cas approach has been used to improve the biotic and abiotic stress tolerance, and traits related to yield and plant architecture have been discussed. The review highlights the challenges to implement the genome editing in polyploid crop plants like wheat, canola, and sugarcane. Challenges for plants difficult to transform and germline-specific gene expression have been discussed. We have also discussed the notable progress with multi-target editing approaches based on polycistronic tRNA processing, Csy4 endoribonuclease, intron processing, and Drosha ribonuclease. Potential to edit multiple targets simultaneously makes it possible to take up more challenging tasks required to engineer desired crop plants. Similarly, advances like precision gene editing, promoter bashing, and methylome-editing will also be discussed. The present review also provides a catalog of available computational tools and servers facilitating designing of guide-RNA targets, construct designs, and data analysis. The information provided here will be useful for the efficient exploration of technological advances in genome editing field for the crop improvement programs.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Virender Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics University of Minnesota, St. Paul, MN 55108-6026, USA.
| | - Trupti Joshi
- Department of Health Management and Informatics; Informatics Institute; Christopher S Bond Life Science Center, University of Missouri, Columbia, MO 65211-7310, USA.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
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11
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Wang H, Wu Y, Zhang Y, Yang J, Fan W, Zhang H, Zhao S, Yuan L, Zhang P. CRISPR/Cas9-Based Mutagenesis of Starch Biosynthetic Genes in Sweet Potato (Ipomoea Batatas) for the Improvement of Starch Quality. Int J Mol Sci 2019; 20:E4702. [PMID: 31547486 PMCID: PMC6801948 DOI: 10.3390/ijms20194702] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas9-mediated genome editing is a powerful technology that has been used for the genetic modification of a number of crop species. In order to evaluate the efficacy of CRISPR/Cas9 technology in the root crop, sweet potato (Ipomoea batatas), two starch biosynthetic pathway genes, IbGBSSI (encoding granule-bound starch synthase I), and IbSBEII (encoding starch branching enzyme II), were targeted in the starch-type cultivar Xushu22 and carotenoid-rich cultivar Taizhong6. I. batatas was transformed using a binary vector, in which the Cas9 gene is driven by the Arabidopsis AtUBQ promoter and the guide RNA is controlled by the Arabidopsis AtU6 promoter. A total of 72 Xushu22 and 35 Taizhong6 transgenic lines were generated and analyzed for mutations. The mutation efficiency was 62-92% with multi-allelic mutations in both cultivars. Most of the mutations were nucleotide substitutions that lead to amino acid changes and, less frequently, stop codons. In addition, short nucleotide insertions or deletions were also found in both IbGBSSI and IbSBEII. Furthermore, a 2658 bp deletion was found in one IbSBEII transgenic line. The total starch contents were not significantly changed in IbGBSSI- and IbSBEII-knockout transgenic lines compared to the wild-type control. However, in the allopolyploid sweet potato, the IbGBSSI-knockout reduced, while the IbSBEII-knockout increased, the amylose percentage. Our results demonstrate that CRISPR/Cas9 technology is an effective tool for the improvement of starch qualities in sweet potato and breeding of polyploid root crops.
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Affiliation(s)
- Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Yinliang Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- Shanghai Sanshu Biotechnology Co., LTD. Shanghai 201210, China.
| | - Yandi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Shanshan Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Ahmad N, Rahman M, Mukhtar Z, Zafar Y, Zhang B. A critical look on CRISPR‐based genome editing in plants. J Cell Physiol 2019; 235:666-682. [DOI: 10.1002/jcp.29052] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/12/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Niaz Ahmad
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Mehboob‐ur Rahman
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Yusuf Zafar
- Pakistan Agriculture Research Council Islamabad Pakistan
| | - Baohong Zhang
- Department of Biology East Carolina University Greenville North Caroline
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13
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Establishment of Efficient Genetic Transformation Systems and Application of CRISPR/Cas9 Genome Editing Technology in Lilium p umilum DC. Fisch. and Lilium l ongiflorum White Heaven. Int J Mol Sci 2019; 20:ijms20122920. [PMID: 31207994 PMCID: PMC6627044 DOI: 10.3390/ijms20122920] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/08/2019] [Accepted: 06/11/2019] [Indexed: 12/24/2022] Open
Abstract
Lilium spp. is a bulb flower with worldwide distribution and unique underground organs. The lack of an efficient genetic transformation system for Lilium has been an international obstacle. Because existing model plants lack bulbs, bulb-related gene function verification studies cannot be carried out in model plants. Here, two stable and efficient genetic transformation systems based on somatic embryogenesis and adventitious bud regeneration were established in two Lilium species. Transgenic plants and T-DNA insertion lines were confirmed by β-glucuronidase (GUS) assay, polymerase chain reaction (PCR) and Southern blot. After condition optimization, transformation efficiencies were increased to 29.17% and 4% in Lilium pumilum DC. Fisch. and the Lilium longiflorum ‘White Heaven’, respectively. To further verify the validity of these transformation systems and apply the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9) technology in Lilium, the LpPDS gene in the two Lilium species was knocked out. Completely albino, pale yellow and albino–green chimeric mutants were observed. Sequence analysis in the transgenic lines revealed various mutation patterns, including base insertion, deletion and substitution. These results verified the feasibility and high efficiency of both transformation systems and the successful application of the CRISPR/Cas9 system to gene editing in Lilium for the first time. Overall, this study lays an important foundation for gene function research and germplasm improvement in Lilium spp.
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Xiong X, Liu W, Jiang J, Xu L, Huang L, Cao J. Efficient genome editing of Brassica campestris based on the CRISPR/Cas9 system. Mol Genet Genomics 2019; 294:1251-1261. [PMID: 31129735 DOI: 10.1007/s00438-019-01564-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/03/2019] [Indexed: 11/28/2022]
Abstract
Conventional methods for gene function study in Brassica campestris have lots of drawbacks, which greatly hinder the identification of important genes' functions and molecular breeding. The clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (CRISPR/Cas9) system is a versatile tool for genome editing that has been widely utilized in many plant species and has many advantages over conventional methods for gene function study. However, the application of CRISPR/Cas9 system in B. campestris remains unreported. The pectin-methylesterase genes Bra003491, Bra007665, and Bra014410 were selected as the targets of the CRISPR/Cas9 system. A single-targeting vector and a multitargeting vector were constructed. Different types of mutations were detected in T0 generation through Agrobacterium transformation. The mutation rate of the three designed sgRNA seeds varied from 20 to 56%. Although the majority of T0 mutants were chimeric, four homozygous mutants were identified. Transformation with the multitargeting vector generated one line with a large fragment deletion and one line with mutations in two target genes. Mutations in Bra003491 were stable and inherited by T1 and T2 generations. Nine mutants which did not contain T-DNA insertions were also obtained. No mutations were detected in predicted potential off-target sites. Our work demonstrated that CRISPR/Cas9 system is efficient on single and multiplex genome editing without off-targeting in B. campestris and that the mutations are stable and inheritable. Our results may greatly facilitate gene functional studies and the molecular breeding of B. campestris and other plants.
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Affiliation(s)
- Xingpeng Xiong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Weimiao Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianxia Jiang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Liai Xu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Li Huang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. .,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
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15
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Zhu S, Yu X, Li Y, Sun Y, Zhu Q, Sun J. Highly Efficient Targeted Gene Editing in Upland Cotton Using the CRISPR/Cas9 System. Int J Mol Sci 2018; 19:E3000. [PMID: 30275376 PMCID: PMC6213220 DOI: 10.3390/ijms19103000] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 01/18/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system has been shown to be able to induce highly efficient mutagenesis in the targeted DNA of many plants, including cotton, and has become an important tool for investigation of gene function and crop improvement. Here, we developed a simple and easy to operate CRISPR/Cas9 system and demonstrated its high editing efficiency in cotton by targeting-ALARP, a gene encoding alanine-rich protein that is preferentially expressed in cotton fibers. Based on sequence analysis of the target site in the 10 transgenic cottons containing CRISPR/Cas9, we found that the mutation frequencies of GhALARP-A and GhALARP-D target sites were 71.4⁻100% and 92.9⁻100%, respectively. The most common editing event was deletion, but deletion together with large insertion was also observed. Mosaic mutation editing events were detected in most transgenic plants. No off-target mutation event was detected in any the 15 predicted sites analyzed. This study provided mutants for further study of the function of GhALARP in cotton fiber development. Our results further demonstrated the feasibility of use of CRISPR/Cas9 as a targeted mutagenesis tool in cotton, and provided an efficient tool for targeted mutagenesis and functional genomics in cotton.
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Affiliation(s)
- Shouhong Zhu
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Xiuli Yu
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Yanjun Li
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Yuqiang Sun
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310016, Zhejiang, China.
| | - Qianhao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra 2601, Australia.
| | - Jie Sun
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
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Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
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Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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17
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Jaganathan D, Ramasamy K, Sellamuthu G, Jayabalan S, Venkataraman G. CRISPR for Crop Improvement: An Update Review. FRONTIERS IN PLANT SCIENCE 2018; 9:985. [PMID: 30065734 PMCID: PMC6056666 DOI: 10.3389/fpls.2018.00985] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/18/2018] [Indexed: 05/06/2023]
Abstract
The availability of genome sequences for several crops and advances in genome editing approaches has opened up possibilities to breed for almost any given desirable trait. Advancements in genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has made it possible for molecular biologists to more precisely target any gene of interest. However, these methodologies are expensive and time-consuming as they involve complicated steps that require protein engineering. Unlike first-generation genome editing tools, CRISPR/Cas9 genome editing involves simple designing and cloning methods, with the same Cas9 being potentially available for use with different guide RNAs targeting multiple sites in the genome. After proof-of-concept demonstrations in crop plants involving the primary CRISPR-Cas9 module, several modified Cas9 cassettes have been utilized in crop plants for improving target specificity and reducing off-target cleavage (e.g., Nmcas9, Sacas9, and Stcas9). Further, the availability of Cas9 enzymes from additional bacterial species has made available options to enhance specificity and efficiency of gene editing methodologies. This review summarizes the options available to plant biotechnologists to bring about crop improvement using CRISPR/Cas9 based genome editing tools and also presents studies where CRISPR/Cas9 has been used for enhancing biotic and abiotic stress tolerance. Application of these techniques will result in the development of non-genetically modified (Non-GMO) crops with the desired trait that can contribute to increased yield potential under biotic and abiotic stress conditions.
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Affiliation(s)
- Deepa Jaganathan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
| | | | | | | | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
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18
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Khan MHU, Khan SU, Muhammad A, Hu L, Yang Y, Fan C. Induced mutation and epigenetics modification in plants for crop improvement by targeting CRISPR/Cas9 technology. J Cell Physiol 2018; 233:4578-4594. [PMID: 29194606 DOI: 10.1002/jcp.26299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced palindromic repeats associated protein Cas9 (CRISPR-Cas9), originally an adaptive immunity system of prokaryotes, is revolutionizing genome editing technologies with minimal off-targets in the present era. The CRISPR/Cas9 is now highly emergent, advanced, and highly specific tool for genome engineering. The technology is widely used to animal and plant genomes to achieve desirable results. The present review will encompass how CRISPR-Cas9 is revealing its beneficial role in characterizing plant genetic functions, genomic rearrangement, how it advances the site-specific mutagenesis, and epigenetics modification in plants to improve the yield of field crops with minimal side-effects. The possible pitfalls of using and designing CRISPR-Cas9 for plant genome editing are also discussed for its more appropriate applications in plant biology. Therefore, CRISPR/Cas9 system has multiple benefits that mostly scientists select for genome editing in several biological systems.
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Affiliation(s)
| | - Shahid U Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ali Muhammad
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Limin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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19
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Zhang Z, Ge X, Luo X, Wang P, Fan Q, Hu G, Xiao J, Li F, Wu J. Simultaneous Editing of Two Copies of Gh14-3-3d Confers Enhanced Transgene-Clean Plant Defense Against Verticillium dahliae in Allotetraploid Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 9:842. [PMID: 30013582 PMCID: PMC6036271 DOI: 10.3389/fpls.2018.00842] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/30/2018] [Indexed: 05/02/2023]
Abstract
Gossypium hirsutum is an allotetraploid species, meaning that mutants that are difficult to be generated by classical approaches due to gene redundancy. The CRISPR/Cas9 genome editing system is a robust and highly efficient tool for generating target gene mutants, by which the genes of interest may be functionally dissected and applied through genotype-to-phenotype approaches. In this study, the CRISPR/Cas9 genome editing system was developed in G. hirsutum through editing the Gh14-3-3d gene. In T0 transgenic plants, lots of insertions and deletions (indels) in Gh14-3-3d at the expected target site were detected in the allotetraploid cotton At or Dt subgenomes. The results of the PCR, T7EI digestion and sequencing analyses showed that the indels in Gh14-3-3d gene can be stably transmitted to the next generation. Additionally, the indels in the At and Dt subgenomes were segregated in the T1 transgenic plants following Mendelian law, independing on the T-DNA segregation. Two homozygous Gh14-3-3d-edited plants free of T-DNA were chosen by PCR and sequencing assays in the T1 plants, which were called transgene-clean editing plants and were designated ce1 and ce2 in the T2 lines showed higher resistance to Verticillium dahliae infestation compared to the wild-type plants. Thus, the two transgene-clean edited lines can be used as a germplasm to breed disease-resistant cotton cultivars, possibly avoiding complex and expensive safety assessments of the transgenic plants.
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Affiliation(s)
- Zhennan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoli Luo
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Peng Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiang Fan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guang Hu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juanli Xiao
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Fuguang Li, Jiahe Wu,
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Fuguang Li, Jiahe Wu,
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20
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Li H, Li K, Guo Y, Guo J, Miao K, Botella JR, Song CP, Miao Y. A transient transformation system for gene characterization in upland cotton ( Gossypium hirsutum). PLANT METHODS 2018; 14:50. [PMID: 29977323 PMCID: PMC6013946 DOI: 10.1186/s13007-018-0319-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/18/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Genetically modified cotton accounts for 64% of the world's cotton growing area (22.3 million hectares). The genome sequencing of the diploid cotton progenitors Gossypium raimondii and Gossypium arboreum as well as the cultivated Gossypium hirsutum has provided a wealth of genetic information that could be exploited for crop improvement. Unfortunately, gene functional characterization in cotton is lagging behind other economically important crops due to the low efficiency, lengthiness and technical complexity of the available stable transformation methods. We present here a simple, fast and efficient method for the transient transformation of G. hirsutum that can be used for gene characterization studies. RESULTS We developed a transient transformation system for gene characterization in upland cotton. Using β-glucuronidase as a reporter for Agrobacterium-mediated transformation assays, we evaluated multiple transformation parameters such as Agrobacterium strain, bacterial density, length of co-cultivation, chemicals and surfactants, which can affect transformation efficiency. After the initial characterization, the Agrobacterium EHA105 strain was selected and a number of binary constructs used to perform gene characterization studies. 7-days-old cotton seedlings were co-cultivated with Agrobacterium and transient gene expression was observed 5 days after infection of the plants. Transcript levels of two different transgenes under the control of the cauliflower mosaic virus (CaMV) 35S promoter were quantified by real-time reverse transcription PCR (qRT-PCR) showing a 3-10 times increase over the levels observed in non-infected controls. The expression patterns driven by the promoters of two G. hirsutum genes as well as the subcellular localization of their corresponding proteins were studied using the new transient expression system and our observations were consistent with previously published results using Arabidopsis as a heterologous system. CONCLUSIONS The Agrobacterium-mediated transient transformation method is a fast and easy transient expression system enabling high transient expression and transformation efficiency in upland cotton seedlings. Our method can be used for gene functional studies such as promoter characterization and protein subcellular localization in cotton, obviating the need to perform such studies in a heterologous system such as Arabidopsis.
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Affiliation(s)
- Haipeng Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Yutao Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Kaiting Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
- School of Life Science, Southwest University, No. 1, Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Jose R. Botella
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD Australia
| | - Chun-Peng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
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21
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Long L, Guo DD, Gao W, Yang WW, Hou LP, Ma XN, Miao YC, Botella JR, Song CP. Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression. PLANT METHODS 2018; 14:85. [PMID: 30305839 PMCID: PMC6169012 DOI: 10.1186/s13007-018-0353-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND When developing CRISPR/Cas9 systems for crops, it is crucial to invest time characterizing the genome editing efficiency of the CRISPR/Cas9 cassettes, especially if the transformation system is difficult or time-consuming. Cotton is an important crop for the production of fiber, oil, and biofuel. However, the cotton stable transformation is usually performed using Agrobacterium tumefaciens taking between 8 and 12 months to generate T0 plants. Furthermore, cotton is a heterotetraploid and targeted mutagenesis is considered to be difficult as many genes are duplicated in this complex genome. The application of CRISPR/Cas9 in cotton is severely hampered by the long and technically challenging genetic transformation process, making it imperative to maximize its efficiency. RESULTS In this study, we provide a new system to evaluate and validate the efficiency of CRISPR/Cas9 cassettes in cotton using a transient expression system. By using this system, we could select the most effective CRISPR/Cas9 cassettes before the stable transformation. We have also optimized the existing cotton CRISPR/Cas9 system to achieve vastly improved mutagenesis efficiency by incorporating an endogenous GhU6 promoter that increases sgRNA expression levels over the Arabidopsis AtU6-29 promoter. The 300 bp GhU6.3 promoter was cloned and validated using the transient expression system. When sgRNAs were expressed under the control of the GhU6.3 promoter in CRISPR/Cas9 cassettes, expression levels were 6-7 times higher than those provided by the AtU6-29 promoter and CRISPR/Cas9-mediated mutation efficiency was improved 4-6 times. CONCLUSIONS This study provides essential improvements to maximize CRISPR/Cas9-mediated mutation efficiency by reducing risk and workload for the application of CRISPR/Cas9 approaches in the targeted mutagenesis of cotton.
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Affiliation(s)
- Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Dan-Dan Guo
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Wen-Wen Yang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Li-Pan Hou
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Yu-Chen Miao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
| | - Jose Ramon Botella
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People’s Republic of China
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22
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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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23
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Jaganathan D, Ramasamy K, Sellamuthu G, Jayabalan S, Venkataraman G. CRISPR for Crop Improvement: An Update Review. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30065734 DOI: 10.3389/fpls.2018.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The availability of genome sequences for several crops and advances in genome editing approaches has opened up possibilities to breed for almost any given desirable trait. Advancements in genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has made it possible for molecular biologists to more precisely target any gene of interest. However, these methodologies are expensive and time-consuming as they involve complicated steps that require protein engineering. Unlike first-generation genome editing tools, CRISPR/Cas9 genome editing involves simple designing and cloning methods, with the same Cas9 being potentially available for use with different guide RNAs targeting multiple sites in the genome. After proof-of-concept demonstrations in crop plants involving the primary CRISPR-Cas9 module, several modified Cas9 cassettes have been utilized in crop plants for improving target specificity and reducing off-target cleavage (e.g., Nmcas9, Sacas9, and Stcas9). Further, the availability of Cas9 enzymes from additional bacterial species has made available options to enhance specificity and efficiency of gene editing methodologies. This review summarizes the options available to plant biotechnologists to bring about crop improvement using CRISPR/Cas9 based genome editing tools and also presents studies where CRISPR/Cas9 has been used for enhancing biotic and abiotic stress tolerance. Application of these techniques will result in the development of non-genetically modified (Non-GMO) crops with the desired trait that can contribute to increased yield potential under biotic and abiotic stress conditions.
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Affiliation(s)
- Deepa Jaganathan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
| | - Karthikeyan Ramasamy
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
| | - Gothandapani Sellamuthu
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
| | - Shilpha Jayabalan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation, Chennai, India
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24
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Phillips AZ, Berry JC, Wilson MC, Vijayaraghavan A, Burke J, Bunn JI, Allen TW, Wheeler T, Bart RS. Genomics-enabled analysis of the emergent disease cotton bacterial blight. PLoS Genet 2017; 13:e1007003. [PMID: 28910288 PMCID: PMC5614658 DOI: 10.1371/journal.pgen.1007003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 09/26/2017] [Accepted: 08/31/2017] [Indexed: 01/09/2023] Open
Abstract
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen Xcm isolates and analyzed along with 4 previously published Xcm genomes. These genomes encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different clade III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal important insights into the Xcm-G. hirsutum disease complex and strategies for future development of resistant cultivars. Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum (Xcm), significantly limited cotton yields in the early 20th century but has been controlled by classical resistance genes for more than 50 years. In 2011, the pathogen re-emerged with a vengeance. In this study, we compare diverse pathogen isolates and cotton varieties to further understand the virulence mechanisms employed by Xcm and to identify promising resistance strategies. We generate fully contiguous genome assemblies for two diverse Xcm strains and identify pathogen proteins used to modulate host transcription and promote susceptibility. RNA-Sequencing of infected cotton reveals novel putative gene targets for the development of durable Xcm resistance. Together, the data presented reveal contributing factors for CBB re-emergence in the U.S. and highlight several promising routes towards the development of durable resistance including classical resistance genes and potential manipulation of susceptibility targets.
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Affiliation(s)
- Anne Z. Phillips
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, United States of America
| | - Jeffrey C. Berry
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | - Mark C. Wilson
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | | | - Jillian Burke
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | - J. Imani Bunn
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | - Tom W. Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States of America
| | - Terry Wheeler
- Texas AgriLife Research, Texas AgriLife Extension Service, Lubbock, TX, United States of America
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
- * E-mail:
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25
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Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci 2017; 7:21. [PMID: 28451378 PMCID: PMC5404292 DOI: 10.1186/s13578-017-0148-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
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Affiliation(s)
- Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - Levi Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850 USA
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26
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Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 DOI: 10.3389/fpls.2017.01364/bibtex] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/20/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
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27
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Gao W, Long L, Tian X, Xu F, Liu J, Singh PK, Botella JR, Song C. Genome Editing in Cotton with the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2017; 8:1364. [PMID: 28824692 PMCID: PMC5541054 DOI: 10.3389/fpls.2017.01364] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 05/17/2023]
Abstract
Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Xinquan Tian
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Fuchun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Prashant K. Singh
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, BrisbaneQLD, Australia
| | - Chunpeng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan UniversityKaifeng, China
- *Correspondence: Chunpeng Song,
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