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Inam S, Muhammad A, Irum S, Rehman N, Riaz A, Uzair M, Khan MR. Genome editing for improvement of biotic and abiotic stress tolerance in cereals. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24092. [PMID: 39222468 DOI: 10.1071/fp24092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems.
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Affiliation(s)
- Safeena Inam
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Amna Muhammad
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Samra Irum
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Nazia Rehman
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Aamir Riaz
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Uzair
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
| | - Muhammad Ramzan Khan
- Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advance Biotechnology (NIGAB), NARC, Park Road, Islamabad 45500, Pakistan
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Wang L, Zhao F, Liu H, Chen H, Zhang F, Li S, Sun T, Nekrasov V, Huang S, Dong S. A modified Agrobacterium-mediated transformation for two oomycete pathogens. PLoS Pathog 2023; 19:e1011346. [PMID: 37083862 PMCID: PMC10156060 DOI: 10.1371/journal.ppat.1011346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 05/03/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Oomycetes are a group of filamentous microorganisms that include some of the biggest threats to food security and natural ecosystems. However, much of the molecular basis of the pathogenesis and the development in these organisms remains to be learned, largely due to shortage of efficient genetic manipulation methods. In this study, we developed modified transformation methods for two important oomycete species, Phytophthora infestans and Plasmopara viticola, that bring destructive damage in agricultural production. As part of the study, we established an improved Agrobacterium-mediated transformation (AMT) method by prokaryotic expression in Agrobacterium tumefaciens of AtVIP1 (VirE2-interacting protein 1), an Arabidopsis bZIP gene required for AMT but absent in oomycetes genomes. Using the new method, we achieved an increment in transformation efficiency in two P. infestans strains. We further obtained a positive GFP transformant of P. viticola using the modified AMT method. By combining this method with the CRISPR/Cas12a genome editing system, we successfully performed targeted mutagenesis and generated loss-of-function mutations in two P. infestans genes. We edited a MADS-box transcription factor-encoding gene and found that a homozygous mutation in MADS-box results in poor sporulation and significantly reduced virulence. Meanwhile, a single-copy avirulence effector-encoding gene Avr8 in P. infestans was targeted and the edited transformants were virulent on potato carrying the cognate resistance gene R8, suggesting that loss of Avr8 led to successful evasion of the host immune response by the pathogen. In summary, this study reports on a modified genetic transformation and genome editing system, providing a potential tool for accelerating molecular genetic studies not only in oomycetes, but also other microorganisms.
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Affiliation(s)
- Luyao Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Fei Zhao
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Haohao Liu
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Han Chen
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Fan Zhang
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Suhua Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tongjun Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Vladimir Nekrasov
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, United Kingdom
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Suomeng Dong
- Department of Plant Pathology and Key Laboratory of Integrated Management of Crop Disease and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
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Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I. An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics 2023; 23:119. [PMID: 37022538 DOI: 10.1007/s10142-023-01036-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.
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Affiliation(s)
- Muhammad Sufyan
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Umar Daraz
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Sajjad Hyder
- Department of Botant, Government College Women University, Sialkot, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo, 11835, Egypt
| | - Farzana Rafiq
- School of Environmental Sciences and Engineering, NCEPU, Beijing, China
| | - Naveed Mahmood
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Khurram Shahzad
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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Rahman SU, McCoy E, Raza G, Ali Z, Mansoor S, Amin I. Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies. Mol Biotechnol 2023; 65:162-180. [PMID: 35119645 DOI: 10.1007/s12033-022-00456-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/21/2022] [Indexed: 01/18/2023]
Abstract
Soybean is considered one of the important crops among legumes. Due to high nutritional contents in seed (proteins, sugars, oil, fatty acids, and amino acids), soybean is used globally for food, feed, and fuel. The primary consumption of soybean is vegetable oil and feed for chickens and livestock. Apart from this, soybean benefits soil fertility by fixing atmospheric nitrogen through root nodular bacteria. While conventional breeding is practiced for soybean improvement, with the advent of new biotechnological methods scientists have also engineered soybean to improve different traits (herbicide, insect, and disease resistance) to fulfill consumer requirements and to meet the global food deficiency. Genetic engineering (GE) techniques such as transgenesis and gene silencing help to minimize the risks and increase the adaptability of soybean. Recently, new plant breeding technologies (NPBTs) emerged such as zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), which paved the way for enhanced genetic modification of soybean. These NPBTs have the potential to improve soybean via gene functional characterization precision genome engineering for trait improvement. Importantly, these NPBTs address the ethical and public acceptance issues related to genetic modifications and transgenesis in soybean. In the present review, we summarized the improvement of soybean through GE and NPBTs. The valuable traits that have been improved through GE for different constraints have been discussed. Moreover, the traits that have been improved through NPBTs and potential targets for soybean improvements via NPBTs and solutions for ethical and public acceptance are also presented.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Evan McCoy
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, USA
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zahir Ali
- Laboratory for Genome Engineering, Center for Desert Agriculture and Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
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Kumar A, Baldia A, Rajput D, Kateriya S, Babu V, Dubey KK. Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery. BIORESOURCE TECHNOLOGY 2023; 369:128457. [PMID: 36503094 DOI: 10.1016/j.biortech.2022.128457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.
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Affiliation(s)
- Akshay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Anshu Baldia
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepanshi Rajput
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vikash Babu
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Kashyap Kumar Dubey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Naz M, Benavides-Mendoza A, Tariq M, Zhou J, Wang J, Qi S, Dai Z, Du D. CRISPR/Cas9 technology as an innovative approach to enhancing the phytoremediation: Concepts and implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116296. [PMID: 36261968 DOI: 10.1016/j.jenvman.2022.116296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Phytoremediation is currently an active field of research focusing chiefly on identifying and characterizing novel and high chelation action super-accumulators. In the last few years, molecular tools have been widely exploited to understand better metal absorption, translocation, cation, and tolerance mechanisms in plants. Recently more advanced CRISPR-Cas9 genome engineering technology is also employed to enhance detoxification efficiency. Further, advances in molecular science will trigger the understanding of adaptive phytoremediation ability plant production in current global warming conditions. The enhanced abilities of nucleases for genome modification can improve plant repair capabilities by modifying the genome, thereby achieving a sustainable ecosystem. The purpose of this manuscript focuses on biotechnology's fundamental principles and application to promote climate-resistant metal plants, especially the CRISPR-Cas9 genome editing system for enhancing the phytoremediation of harmful contamination and pollutants.
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Affiliation(s)
- Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Adalberto Benavides-Mendoza
- Department of Horticulture, Autonomous Agricultural University Antonio Narro, 1923 Saltillo, C.P. 25315, Mexico
| | - Muhammad Tariq
- Department of Pharmacology, Lahore Pharmacy College, 54000, Lahore, Pakistan
| | - Jianyu Zhou
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Shanshan Qi
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Zhicong Dai
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, 99 Xuefu Road, Suzhou, 215009, Jiangsu Province, PR China.
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
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Ul Haq SI, Zheng D, Feng N, Jiang X, Qiao F, He JS, Qiu QS. Progresses of CRISPR/Cas9 genome editing in forage crops. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153860. [PMID: 36371870 DOI: 10.1016/j.jplph.2022.153860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.
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Affiliation(s)
- Syed Inzimam Ul Haq
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Feng Qiao
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China; Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
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Kumar K, Mandal SN, Pradhan B, Kaur P, Kaur K, Neelam K. From Evolution to Revolution: Accelerating Crop Domestication through Genome Editing. PLANT & CELL PHYSIOLOGY 2022; 63:1607-1623. [PMID: 36018059 DOI: 10.1093/pcp/pcac124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Crop domestication has a tremendous impact on socioeconomic conditions and human civilization. Modern cultivars were domesticated from their wild progenitors thousands of years ago by the selection of natural variation by humans. New cultivars are being developed by crossing two or more compatible individuals. But the limited genetic diversity in the cultivars severely affects the yield and renders the crop susceptible to many biotic and abiotic stresses. Crop wild relatives (CWRs) are the rich reservoir for many valuable agronomic traits. The incorporation of useful genes from CWR is one of the sustainable approaches for enriching the gene pool of cultivated crops. However, CWRs are not suited for urban and intensive cultivation because of several undesirable traits. Researchers have begun to study the domestication traits in the CWRs and modify them using genome-editing tools to make them suitable for extensive cultivation. Growing evidence has shown that modification in these genes is not sufficient to bring the desired change in the neodomesticated crop. However, the other dynamic genetic factors such as microRNAs (miRNAs), transposable elements, cis-regulatory elements and epigenetic changes have reshaped the domesticated crops. The creation of allelic series for many valuable domestication traits through genome editing holds great potential for the accelerated development of neodomesticated crops. The present review describes the current understanding of the genetics of domestication traits that are responsible for the agricultural revolution. The targeted mutagenesis in these domestication genes via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 could be used for the rapid domestication of CWRs.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Swarupa Nanda Mandal
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79415, USA
| | - Bhubaneswar Pradhan
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Pavneet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Karminderbir Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
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11
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Advanced Breeding for Biotic Stress Resistance in Poplar. PLANTS 2022; 11:plants11152032. [PMID: 35956510 PMCID: PMC9370193 DOI: 10.3390/plants11152032] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 12/20/2022]
Abstract
Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.
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12
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Fan S, Zhang Z, Song Y, Zhang J, Wang P. CRISPR/Cas9-mediated targeted mutagenesis of GmTCP19L increasing susceptibility to Phytophthora sojae in soybean. PLoS One 2022; 17:e0267502. [PMID: 35679334 PMCID: PMC9182224 DOI: 10.1371/journal.pone.0267502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 04/10/2022] [Indexed: 11/18/2022] Open
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors is one of the superfamilies of plant-specific transcription factors involved in plant growth, development, and biotic and abiotic stress. However, there is no report on the research of the TCP transcription factors in soybean response to Phytophthora sojae. In this study, Agrobacterium-mediated transformation was used to introduce the CRISPR/Cas9 expression vector into soybean cultivar "Williams 82" and generated targeted mutants of GmTCP19L gene, which was previously related to involve in soybean responses to P. sojae. We obtained the tcp19l mutants with 2-bp deletion at GmTCP19L coding region, and the frameshift mutations produced premature translation termination codons and truncated GmTCP19L proteins, increasing susceptibility to P. sojae in the T2-generation. These results suggest that GmTCP19L encodes a TCP transcription factor that affects plant defense in soybean. The new soybean germplasm with homozygous tcp19l mutations but the BAR and Cas9 sequences were undetectable using strip and PCR methods, respectively, suggesting directions for the breeding or genetic engineering of disease-resistant soybean plants.
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Affiliation(s)
- Sujie Fan
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People’s Republic of China
- Crop Science Post-doctoral Station, Jilin Agricultural University, Changchun, Jilin, People’s Republic of China
| | - Zhuo Zhang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People’s Republic of China
| | - Yang Song
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People’s Republic of China
| | - Jun Zhang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People’s Republic of China
| | - Piwu Wang
- Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, People’s Republic of China
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13
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Salgotra RK, Thompson M, Chauhan BS. Unravelling the genetic potential of untapped crop wild genetic resources for crop improvement. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Sharma S, Sanyal SK, Sushmita K, Chauhan M, Sharma A, Anirudhan G, Veetil SK, Kateriya S. Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops. Curr Genomics 2021; 22:181-213. [PMID: 34975290 PMCID: PMC8640849 DOI: 10.2174/1389202922666210412104817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022] Open
Abstract
Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.
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Affiliation(s)
- Sunita Sharma
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sibaji K. Sanyal
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kumari Sushmita
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Gireesh Anirudhan
- Integrated Science Education and Research Centre (ISERC), Institute of Science (Siksha Bhavana), Visva Bharati (A Central University), Santiniketan (PO), West Bengal, 731235, India
| | - Sindhu K. Veetil
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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15
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Citiulo F, Crosatti C, Cattivelli L, Biselli C. Frontiers in the Standardization of the Plant Platform for High Scale Production of Vaccines. PLANTS (BASEL, SWITZERLAND) 2021; 10:1828. [PMID: 34579360 PMCID: PMC8467261 DOI: 10.3390/plants10091828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
The recent COVID-19 pandemic has highlighted the value of technologies that allow a fast setup and production of biopharmaceuticals in emergency situations. The plant factory system can provide a fast response to epidemics/pandemics. Thanks to their scalability and genome plasticity, plants represent advantageous platforms to produce vaccines. Plant systems imply less complicated production processes and quality controls with respect to mammalian and bacterial cells. The expression of vaccines in plants is based on transient or stable transformation systems and the recent progresses in genome editing techniques, based on the CRISPR/Cas method, allow the manipulation of DNA in an efficient, fast, and easy way by introducing specific modifications in specific sites of a genome. Nonetheless, CRISPR/Cas is far away from being fully exploited for vaccine expression in plants. In this review, an overview of the potential conjugation of the renewed vaccine technologies (i.e., virus-like particles-VLPs, and industrialization of the production process) with genome editing to produce vaccines in plants is reported, illustrating the potential advantages in the standardization of the plant platforms, with the overtaking of constancy of large-scale production challenges, facilitating regulatory requirements and expediting the release and commercialization of the vaccine products of genome edited plants.
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Affiliation(s)
- Francesco Citiulo
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy;
| | - Cristina Crosatti
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.C.); (L.C.)
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.C.); (L.C.)
| | - Chiara Biselli
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Viale Santa Margherita 80, 52100 Arezzo, Italy
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16
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Butiuc-Keul A, Farkas A, Carpa R, Iordache D. CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes. Microb Physiol 2021; 32:2-17. [PMID: 34192695 DOI: 10.1159/000516643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.
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Affiliation(s)
- Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Anca Farkas
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Rahela Carpa
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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17
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Biswas S, Zhang D, Shi J. CRISPR/Cas systems: opportunities and challenges for crop breeding. PLANT CELL REPORTS 2021; 40:979-998. [PMID: 33977326 DOI: 10.1007/s00299-021-02708-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/28/2021] [Indexed: 05/27/2023]
Abstract
Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.
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Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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18
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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19
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20
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Das A, Ghana P, Rudrappa B, Gandhi R, Tavva VS, Mohanty A. Genome Editing of Rice by CRISPR-Cas: End-to-End Pipeline for Crop Improvement. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2238:115-134. [PMID: 33471328 DOI: 10.1007/978-1-0716-1068-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas resonates a revolutionary genome editing technology applicable through a horizon spreading across microbial organism to higher plant and animal. This technology can be harnessed with ease to understand the basic genetics of a living system by altering sequence of individual genes and characterizing their functions. The precision of this technology is unparallel. It allows very precise and targeted base pair level edits in the genome. Here, in the current chapter, we have provided end-to-end process outline on how to generate genome edited plants in crops like rice to evaluate for agronomic traits associated with yield, disease resistance and abiotic stress tolerance, etc. Genome editing process includes designing of gene editing strategy, vector construction, plant transformation, molecular screening, and phenotyping under control environment conditions. Furthermore, its application for development of commercial crop product may require additional processes, including field trials in the target geography for evaluation of product efficacy. Evaluation of genome edited lines in controlled greenhouse/net house or open field condition requires few generations for outcrossing with wild-type parent to eliminate and/or reduce any potential pleiotropic effect in the edited genome which may arise during the process. The genome edited plant selected for advancement shall harbor the genome with only the intended changes, which can be analyzed by various molecular techniques, advanced sequencing methods, and genomic data analysis tools. CRISPR-Cas-based genome editing has opened a plethora of opportunities in agriculture as well as human health.
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Affiliation(s)
- Amit Das
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India
| | - Pallavi Ghana
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India
| | - Bhojaraja Rudrappa
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India
| | - Rita Gandhi
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India
| | - Venkata Sresty Tavva
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India
| | - Amitabh Mohanty
- Formerly at Corteva Agriscience™, DuPont Knowledge Centre, Hyderabad, Telangana, India. .,Corteva Agriscience , Johnston, IA-50131, USA.
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21
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Pujari I, Thomas A, Rai PS, Satyamoorthy K, Babu VS. Cell size: a key determinant of meristematic potential in plant protoplasts. ABIOTECH 2021; 2:96-104. [PMID: 36304480 PMCID: PMC9590549 DOI: 10.1007/s42994-020-00033-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/18/2020] [Indexed: 06/16/2023]
Abstract
Metabolic pathway reconstruction and gene edits for native natural product synthesis in single plant cells are considered to be less complicated when compared to the production of non-native metabolites. Being an efficient eukaryotic system, plants encompass suitable post-translational modifications. However, slow cell division rate and heterogeneous nature is an impediment for consistent product retrieval from plant cells. Plant cell synchrony can be attained in cultures developed in vitro. Isolated plant protoplasts capable of division, can potentially enhance the unimpaired yield of target bioactives, similar to microbes and unicellular eukaryotes. Evidence from yeast experiments suggests that 'critical cell size' and division rates for enhancement machinery, primarily depend on culture conditions and nutrient availability. The cell size control mechanisms in Arabidopsis shoot apical meristem is analogous to yeast notably, fission yeast. If protoplasts isolated from plants are subjected to cell size studies and cell cycle progression in culture, it will answer the underlying molecular mechanisms such as, unicellular to multicellular transition states, longevity, senescence, 'cell-size resetting' during organogenesis, and adaptation to external cues.
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Affiliation(s)
- Ipsita Pujari
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
| | - Abitha Thomas
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
| | - Padmalatha S. Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Vidhu Sankar Babu
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
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22
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Zhang L, Wang Y, Li T, Qiu H, Xia Z, Dong Y. Target-specific mutations efficiency at multiple loci of CRISPR/Cas9 system using one sgRNA in soybean. Transgenic Res 2021; 30:51-62. [PMID: 33387102 DOI: 10.1007/s11248-020-00228-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022]
Abstract
Soybean has a palaeopolyploid genome with nearly 75% of the genes present in multiple copies. Although the CRISPR/Cas9 system has been employed in soybean to generate site-directed mutagenesis, a systematical assessment of mutation efficiency of the CRISPR/Cas9 system for the multiple-copy genes is still urgently needed. Here, we successfully optimize one sgRNA CRISPR/Cas9 system in soybean by testing the efficiency, pattern, specificity of the mutations at multiple loci of GmFAD2 and GmALS. The results showed that simultaneous site-directed mutagenesis of two homoeologous loci by one sgRNA, the mutation frequency in the T0 generation were 64.71% for GmPDS, 60.0% for GmFAD2 and 42.86% for GmALS, respectively. The chimeric and heterozygous mutations were dominant types. Moreover, association of phenotypes with mutation pattern at target loci of GmPDS11 and GmPDS18 could help us further demonstrate that the CRISPR/Cas9 system can efficiently generate target specific mutations at multiple loci using one sgRNA in soybean, albeit with a relatively low transformation efficiency.
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Affiliation(s)
- Ling Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Yingzhe Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Tong Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Hongmei Qiu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China
| | - Zhengjun Xia
- Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin, China.
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23
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Shipman EN, Yu J, Zhou J, Albornoz K, Beckles DM. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? HORTICULTURE RESEARCH 2021; 8:1. [PMID: 33384412 PMCID: PMC7775472 DOI: 10.1038/s41438-020-00428-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/22/2023]
Abstract
Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR-Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are "ripe" for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5-10 years.
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Affiliation(s)
- Emma N Shipman
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA.
| | - Jingwei Yu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA.
| | - Karin Albornoz
- Departamento de Produccion Vegetal, Universidad de Concepcion, Region del BioBio, Concepcion, Chile.
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Van Eck J. Applying gene editing to tailor precise genetic modifications in plants. J Biol Chem 2020; 295:13267-13276. [PMID: 32723863 PMCID: PMC7504920 DOI: 10.1074/jbc.rev120.010850] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/27/2020] [Indexed: 12/26/2022] Open
Abstract
The ability to tailor alterations in genomes, including plant genomes, in a site-specific manner has been greatly advanced through approaches that reduced the complexity and time of genome sequencing along with development of gene editing technologies. These technologies provide a valuable foundation for studies of gene function, metabolic engineering, and trait modification for crop improvement. Development of genome editing methodologies began ∼20 years ago, first with meganucleases and followed by zinc finger nucleases, transcriptional activator-like effector nucleases and, most recently, clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas) (CRISPR/Cas), which is by far the most utilized method. The premise of CRISPR/Cas centers on the cleaving of one or both DNA strands by a Cas protein, an endonuclease, followed by mending of the DNA by repair mechanisms inherent in cells. Its user-friendly construct design, greater flexibility in targeting genomic regions, and cost-effective attributes have resulted in it being widely adopted and revolutionizing precise modification of the genomes of many organisms. Indeed, the CRISPR/Cas system has been utilized for gene editing in many plant species, including important food crops, such as maize, wheat, rice, and potatoes. This review summarizes the various approaches, including the most recent designs being used to make modifications from as small as a single-base-pair change to insertion of DNA fragments. On the gene expression level, strategies are presented that make it possible to knock out or modulate through activation and repression. Also discussed are prerequisites necessary for CRISPR/Cas-mediated editing as well as the current challenges.
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Affiliation(s)
- Joyce Van Eck
- Boyce Thompson Institute, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA.
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Sudheer S, Bai RG, Usmani Z, Sharma M. Insights on Engineered Microbes in Sustainable Agriculture: Biotechnological Developments and Future Prospects. Curr Genomics 2020; 21:321-333. [PMID: 33093796 PMCID: PMC7536804 DOI: 10.2174/1389202921999200603165934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/05/2020] [Accepted: 04/19/2020] [Indexed: 02/08/2023] Open
Abstract
Background Enhanced agricultural production is essential for increasing demand of the growing world population. At the same time, to combat the adverse effects caused by conventional agriculture practices to the environment along with the impact on human health and food security, a sustainable and healthy agricultural production needs to be practiced using beneficial microorganisms for enhanced yield. It is quite challenging because these microorganisms have rich biosynthetic repositories to produce biomolecules of interest; however, the intensive research in allied sectors and emerging genetic tools for improved microbial consortia are accepting new approaches that are helpful to farmers and agriculturists to meet the ever-increasing demand of sustainable food production. An important advancement is improved strain development via genetically engineered microbial systems (GEMS) as well as genetically modified microorganisms (GMOs) possessing known and upgraded functional characteristics to promote sustainable agriculture and food security. With the development of novel technologies such as DNA automated synthesis, sequencing and influential computational tools, molecular biology has entered the systems biology and synthetic biology era. More recently, CRISPR/Cas has been engineered to be an important tool in genetic engineering for various applications in the agri sector. The research in sustainable agriculture is progressing tremendously through GMOs/GEMS for their potential use in biofertilizers and as biopesticides. Conclusion In this review, we discuss the beneficial effects of engineered microorganisms through integrated sustainable agriculture production practices to improve the soil microbial health in order to increase crop productivity.
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Affiliation(s)
- Surya Sudheer
- 1Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 2School of Natural Sciences and Health, Tallinn University, Narva mnt 29, Tallinn10120, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Department of Food Technology, ACA, Eternal University, Baru Sahib, 173001, Himachal Pradesh, India
| | - Renu Geetha Bai
- 1Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 2School of Natural Sciences and Health, Tallinn University, Narva mnt 29, Tallinn10120, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Department of Food Technology, ACA, Eternal University, Baru Sahib, 173001, Himachal Pradesh, India
| | - Zeba Usmani
- 1Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 2School of Natural Sciences and Health, Tallinn University, Narva mnt 29, Tallinn10120, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Department of Food Technology, ACA, Eternal University, Baru Sahib, 173001, Himachal Pradesh, India
| | - Minaxi Sharma
- 1Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 2School of Natural Sciences and Health, Tallinn University, Narva mnt 29, Tallinn10120, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Department of Food Technology, ACA, Eternal University, Baru Sahib, 173001, Himachal Pradesh, India
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CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10071033] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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Biswas S, Tian J, Li R, Chen X, Luo Z, Chen M, Zhao X, Zhang D, Persson S, Yuan Z, Shi J. Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding. J Genet Genomics 2020; 47:273-280. [PMID: 32684419 DOI: 10.1016/j.jgg.2020.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
Abstract
Although Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has been widely used for basic research in model plants, its application for applied breeding in crops has faced strong regulatory obstacles, due mainly to a poor understanding of the authentic output of this system, particularly in higher generations. In this study, different from any previous studies, we investigated in detail the molecular characteristics and production performance of CRISPR/Cas9-generated SD1 (semi-dwarf 1) mutants from T2 to T4 generations, of which the selection of T1 and T2 was done only by visual phenotyping for semidwarf plants. Our data revealed not only on- and off-target mutations with small or lager indels but also exogenous elements in T2 plants. All indel mutants passed stably to T3 or T4 without additional modifications independent on the presence of Cas9, while some lines displayed unexpected hereditary patterns of Cas9 or some exogenous elements. In addition, effects of various SD1 alleles on rice height and yield differed depending on genetic backgrounds. Taken together, our data showed that the CRISPR/Cas9 system is effective in producing homozygous mutants for functional analysis, but it may be not as precise as expected in rice, and that early and accurate molecular characterization and screening must be carried out for generations before transitioning of the CRISPR/Cas9 system from laboratory to field.
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Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiaqi Tian
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiangxiang Zhao
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Biosciences, University of Melbourne, Parkville VIC, 3010, Melbourne, Australia
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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29
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Campos ML, Prado GS, Dos Santos VO, Nascimento LC, Dohms SM, da Cunha NB, Ramada MHS, Grossi-de-Sa MF, Dias SC. Mosses: Versatile plants for biotechnological applications. Biotechnol Adv 2020; 41:107533. [PMID: 32151692 DOI: 10.1016/j.biotechadv.2020.107533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/03/2023]
Abstract
Mosses have long been recognized as powerful experimental tools for the elucidation of complex processes in plant biology. Recent increases in the availability of sequenced genomes and mutant collections, the establishment of novel technologies for targeted mutagenesis, and the development of viable protocols for large-scale production in bioreactors are now transforming mosses into one of the most versatile tools for biotechnological applications. In the present review, we highlight the astonishing biotechnological potential of mosses and how these plants are being exploited for industrial, pharmaceutical, and environmental applications. We focus on the biological features that support their use as model organisms for basic and applied research, and how these are being leveraged to explore the biotechnological potential in an increasing number of species. Finally, we also provide an overview of the available moss cultivation protocols from an industrial perspective, offering insights into batch operations that are not yet well established or do not even exist in the literature. Our goal is to bolster the use of mosses as factories for the biosynthesis of molecules of interest and to show how these species can be harnessed for the generation of novel and commercially useful bioproducts.
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Affiliation(s)
- Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| | - Guilherme Souza Prado
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Vanessa Olinto Dos Santos
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Lara Camelo Nascimento
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Stephan Machado Dohms
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Nicolau Brito da Cunha
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Marcelo Henrique Soller Ramada
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Maria Fatima Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
| | - Simoni Campos Dias
- Centro de Análises Bioquímicas e Proteômicas, Universidade Católica de Brasília, Brasilia, DF, Brazil; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Biologia Animal, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil.
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30
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Bruznican S, De Clercq H, Eeckhaut T, Van Huylenbroeck J, Geelen D. Celery and Celeriac: A Critical View on Present and Future Breeding. FRONTIERS IN PLANT SCIENCE 2020; 10:1699. [PMID: 32038678 PMCID: PMC6987470 DOI: 10.3389/fpls.2019.01699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Cultivated for the crispy petioles and round, fleshy, and flavored hypocotyl celery and celeriac have over two centuries of breeding history in Europe. In this review paper we summarized the most recent advances touching when necessary the historical context of celery and celeriac breeding. In the post genomic era of research, the genome sequence of celery is only partially available. We comprised however in this paper the most important aspects of celery genetics that are available today and have applicability in celery modern cultivars development. We discussed the problems and traits that drive the main celery and celeriac breeding goals, like hybrid seed production, disease resistance, and interesting enlarged hypocotyl and petiole characteristics. Besides the classical breeding traits we covered the potential of integration of existing cultivars as sources for consumer oriented traits like nutraceuticals and health promoting substances. Sustainability is a subject that is continuously growing in popularity and we looked at the genetic base of celery and celeriac that makes them sources for abiotic stress resistance and candidates for phytoremediation. We explored the fundamental concepts gained in various fields of celery and related species research, as resources for future improvement of celery and celeriac germplasm. We forecast what the next years will bring to Apium breeding.
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Affiliation(s)
- Silvia Bruznican
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Production, Ghent University, Ghent, Belgium
| | - Hervé De Clercq
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Eeckhaut
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Johan Van Huylenbroeck
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Danny Geelen
- Department of Plant Production, Ghent University, Ghent, Belgium
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31
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Moradpour M, Abdulah SNA. CRISPR/dCas9 platforms in plants: strategies and applications beyond genome editing. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:32-44. [PMID: 31392820 PMCID: PMC6920162 DOI: 10.1111/pbi.13232] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) and Cas9-associated protein systems provide a powerful genetic manipulation tool that can drive plant research forward. Nuclease-dead Cas9 (dCas9) is an enzymatically inactive mutant of Cas9 in which its endonuclease activity is non-functional. The applications of CRISPR/dCas9 have expanded and diversified in recent years. Originally, dCas9 was used as a CRISPR/Cas9 re-engineering tool that enables targeted expression of any gene or multiple genes through recruitment of transcriptional effector domains without introducing irreversible DNA-damaging mutations. Subsequent applications have made use of its ability to recruit modifying enzymes and reporter proteins to DNA target sites. In this paper, the most recent progress in the applications of CRISPR/dCas9 in plants, which include gene activation and repression, epigenome editing, modulation of chromatin topology, live-cell chromatin imaging and DNA-free genetic modification, will be reviewed. The associated strategies for exploiting the CRISPR/dCas9 system for crop improvement with a dimer of the future of the CRISPR/dCas9 system in the functional genomics of crops and the development of traits will be briefly discussed.
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Affiliation(s)
- Mahdi Moradpour
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Siti Nor Akmar Abdulah
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Department of Agricultural TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangSelangorMalaysia
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32
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Manghwar H, Lindsey K, Zhang X, Jin S. CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. TRENDS IN PLANT SCIENCE 2019; 24:1102-1125. [PMID: 31727474 DOI: 10.1016/j.tplants.2019.09.006] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [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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33
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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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New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering. Biotechnol Adv 2019; 37:107371. [PMID: 30890361 DOI: 10.1016/j.biotechadv.2019.03.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.
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Manna I, Bandyopadhyay M. A review on the biotechnological aspects of utilizing engineered nanoparticles as delivery systems in plants. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2018.100167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Zimny T, Sowa S, Tyczewska A, Twardowski T. Certain new plant breeding techniques and their marketability in the context of EU GMO legislation - recent developments. N Biotechnol 2019; 51:49-56. [PMID: 30779963 DOI: 10.1016/j.nbt.2019.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/04/2019] [Accepted: 02/09/2019] [Indexed: 12/20/2022]
Abstract
The comparatively low adoption rate of GMO products in the European Union (EU) market seems to be connected with the strictness of authorization regulations and inefficiency of the authorization process itself. These problems will apply to any product deemed to be a GMO that could potentially be marketable in the EU. Since modern methods of plant breeding involving oligonucleotide-directed mutagenesis (ODMs) or site-directed nucleases (SDNs), including Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are becoming ever more popular, it is crucial to establish whether the products of such new breeding techniques (NBTs), in particular those which involve precise methods of mutagenesis, are exempted from the EU legislation on GMOs or not. Legal uncertainty as to their status may result in reluctance to invest in such methods and develop them further. Here, developments are presented in the legal classification of certain NBTs products in the context of recent decisions and jurisprudence. The socioeconomic aspects of GMO adoption in both global and European contexts are discussed. The legal and practical landscape of GMO regulation in the EU is presented and how it may pose an obstacle to investment and the development of new products. The latest jurisprudence (e.g., Case C-528/16) [1] on the interpretation of the legal concept of GMOs and the scope of the legislation are analyzed, with the conclusion that the strict regulations will probably also apply to products of the NBTs involving precise methods of mutagenesis. This in turn will probably result in the restriction of their application in the development of new plant varieties in the EU.
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Affiliation(s)
- Tomasz Zimny
- Institute of Law Studies, Polish Academy of Sciences, Warszawa, Poland.
| | - Sławomir Sowa
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland.
| | - Agata Tyczewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
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Current situation of biofuel production and its enhancement by CRISPR/Cas9-mediated genome engineering of microbial cells. Microbiol Res 2019; 219:1-11. [DOI: 10.1016/j.micres.2018.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/10/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022]
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Xu J, Hua K, Lang Z. Genome editing for horticultural crop improvement. HORTICULTURE RESEARCH 2019; 6:113. [PMID: 31645967 PMCID: PMC6804600 DOI: 10.1038/s41438-019-0196-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/18/2019] [Accepted: 08/13/2019] [Indexed: 05/06/2023]
Abstract
Horticultural crops provide humans with many valuable products. The improvement of the yield and quality of horticultural crops has been receiving increasing research attention. Given the development and advantages of genome-editing technologies, research that uses genome editing to improve horticultural crops has substantially increased in recent years. Here, we briefly review the different genome-editing systems used in horticultural research with a focus on clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-mediated genome editing. We also summarize recent progress in the application of genome editing for horticultural crop improvement. The combination of rapidly advancing genome-editing technology with breeding will greatly increase horticultural crop production and quality.
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Affiliation(s)
- Jiemeng Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Kai Hua
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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Foyer CH, Siddique KHM, Tai APK, Anders S, Fodor N, Wong FL, Ludidi N, Chapman MA, Ferguson BJ, Considine MJ, Zabel F, Prasad PVV, Varshney RK, Nguyen HT, Lam HM. Modelling predicts that soybean is poised to dominate crop production across Africa. PLANT, CELL & ENVIRONMENT 2019; 42:373-385. [PMID: 30329164 DOI: 10.1111/pce.13466] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/08/2018] [Accepted: 10/14/2018] [Indexed: 05/22/2023]
Abstract
The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume-based farming is particularly important in Africa, where small-scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land-use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful "soybean bonanza" across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.
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Affiliation(s)
- Christine H Foyer
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Molecular Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Amos P K Tai
- Earth System Science Programme, The Chinese University of Hong Kong, Shatin, Hong Kong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sven Anders
- Department of Resource Economics and Environmental Sociology, University of Alberta, Edmonton, Alberta, Canada
| | - Nándor Fodor
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Centre for Agricultural Research, Hungarian Academy of Sciences, Agricultural Institute, Martonvásár, Hungary
| | - Fuk-Ling Wong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ndiko Ludidi
- Department of Biotechnology and the DST/NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, UK
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael J Considine
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Molecular Science, The University of Western Australia, Perth, Western Australia, Australia
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Florian Zabel
- Ludwig-Maximilians-Universität München, Munich, Germany
| | - P V Vara Prasad
- Department of Agronomy, College of Agriculture, Kansas State University, Manhattan, Kansas, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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40
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Kumlehn J, Pietralla J, Hensel G, Pacher M, Puchta H. The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1127-1153. [PMID: 30387552 DOI: 10.1111/jipb.12734] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
Since the discovery that nucleases of the bacterial CRISPR (clustered regularly interspaced palindromic repeat)-associated (Cas) system can be used as easily programmable tools for genome engineering, their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction, resulting in mutations by non-homologous recombination. Strategies for performing such experiments - from the design of guide RNA to the use of different transformation technologies - are evaluated. Furthermore, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNA-binding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.
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Affiliation(s)
- Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Janine Pietralla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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41
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Busov VB. Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production. FRONTIERS IN PLANT SCIENCE 2018; 9:1505. [PMID: 30459780 PMCID: PMC6232754 DOI: 10.3389/fpls.2018.01505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Growth and architectural traits in trees are economically and environmentally important and thus of considerable importance to the improvement of forest and fruit trees. These traits are complex and result from the operation of a number of molecular mechanisms. This review will focus on the regulation of crown architecture, secondary woody growth and adventitious rooting. These traits and processes have significant impact on deployment, management, and productivity of tree crops. The majority of the described work comes from experiments in model plants, poplar, apple, peach, and plum because these species allow functional analysis of the involved genes and have significant genomics resources. However, these studies convincingly show conserved mechanisms for elaboration of specific growth and architectural traits. The conservation of these mechanisms suggest that they can be used as a blueprint for the improvement of these traits and processes in phylogenetically diverse tree crops. We will specifically consider the involvement of flowering time, transcription factors and hormone-associated genes. The review will also discuss the impact of recent technological advances as well as the challenges to the dissection of these traits in trees.
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42
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Fasani E, Manara A, Martini F, Furini A, DalCorso G. The potential of genetic engineering of plants for the remediation of soils contaminated with heavy metals. PLANT, CELL & ENVIRONMENT 2018; 41:1201-1232. [PMID: 28386947 DOI: 10.1111/pce.12963] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/06/2017] [Accepted: 03/28/2017] [Indexed: 05/22/2023]
Abstract
The genetic engineering of plants to facilitate the reclamation of soils and waters contaminated with inorganic pollutants is a relatively new and evolving field, benefiting from the heterologous expression of genes that increase the capacity of plants to mobilize, stabilize and/or accumulate metals. The efficiency of phytoremediation relies on the mechanisms underlying metal accumulation and tolerance, such as metal uptake, translocation and detoxification. The transfer of genes involved in any of these processes into fast-growing, high-biomass crops may improve their reclamation potential. The successful phytoextraction of metals/metalloids and their accumulation in aerial organs have been achieved by expressing metal ligands or transporters, enzymes involved in sulfur metabolism, enzymes that alter the chemical form or redox state of metals/metalloids and even the components of primary metabolism. This review article considers the potential of genetic engineering as a strategy to improve the phytoremediation capacity of plants in the context of heavy metals and metalloids, using recent case studies to demonstrate the practical application of this approach in the field.
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Affiliation(s)
- Elisa Fasani
- Department of Biotechnology, University of Verona, St. Le Grazie 15, Verona, 37134, Italy
| | - Anna Manara
- Department of Biotechnology, University of Verona, St. Le Grazie 15, Verona, 37134, Italy
| | - Flavio Martini
- Department of Biotechnology, University of Verona, St. Le Grazie 15, Verona, 37134, Italy
| | - Antonella Furini
- Department of Biotechnology, University of Verona, St. Le Grazie 15, Verona, 37134, Italy
| | - Giovanni DalCorso
- Department of Biotechnology, University of Verona, St. Le Grazie 15, Verona, 37134, Italy
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43
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Islam W. CRISPR-Cas9; an efficient tool for precise plant genome editing. Mol Cell Probes 2018; 39:47-52. [PMID: 29621557 DOI: 10.1016/j.mcp.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 01/09/2023]
Abstract
Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, I have tried to sum up the application of this biotechnological tool in plant genome editing. Furthermore, I have tried to explain successful adaptation of CRISPR in various plant species where it is used for the successful generation of stable mutations in a steadily growing number of species through NHEJ. The review also sheds light upon other biotechnological approaches relying upon single DNA lesion induction such as genomic deletion or pair wise nickases for evasion of offsite effects.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Govt.of Punjab, Agriculture Department, Lahore, Pakistan.
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44
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Jouanin A, Boyd L, Visser RGF, Smulders MJM. Development of Wheat With Hypoimmunogenic Gluten Obstructed by the Gene Editing Policy in Europe. FRONTIERS IN PLANT SCIENCE 2018; 9:1523. [PMID: 30405661 PMCID: PMC6200864 DOI: 10.3389/fpls.2018.01523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/27/2018] [Indexed: 05/05/2023]
Abstract
Coeliac Disease (CD) is an auto-immune reaction to gluten in 1-2% of the human population. A gluten-free (GF) diet, excluding wheat, barley, and rye, is the only remedy. This diet is difficult to adhere to, partly because wheat gluten is added to many processed products for their viscoelastic properties. In addition, GF products are less healthy and expensive. Wheat products containing only hypoimmunogenic gluten proteins would be a desirable option. Various gluten peptides that trigger CD have been characterized. A single wheat variety contains around hundred gluten genes, producing proteins with varying numbers of epitopes. Gene editing using CRISPR/Cas9 can precisely remove or modify the DNA sequences coding for immunogenic peptides. Wheat with hypoimmunogenic gluten thus exemplifies the potential of gene editing for improving crops for human consumption where conventional breeding cannot succeed. We describe here, in relation to breeding hypoimmunogenic wheat varieties, the inconsistencies of applying GM regulation in Europe for gene-edited plants while mutation breeding-derived plants are exempted. We explain that healthy products derived from this new technology may become available in the United States, Canada, Argentina and other countries but not in Europe, because of strict regulation of unintended GM risk at the expense of reduction the existing immunogenicity risks of patients. We argue that regulation of gene-edited plants should be based on scientific evidence. Therefore, we strongly recommend implementing the innovation principle. Responsible Research and Innovation, involving stakeholders including CD patient societies in the development of gene-editing products, will enable progress toward healthy products and encourage public acceptance.
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Affiliation(s)
- Aurélie Jouanin
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Genetics & Breeding Research, National Institute of Agricultural Botany, Cambridge, United Kingdom
- *Correspondence: Aurélie Jouanin, Marinus J. M. Smulders,
| | - Lesley Boyd
- Genetics & Breeding Research, National Institute of Agricultural Botany, Cambridge, United Kingdom
| | | | - Marinus J. M. Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Aurélie Jouanin, Marinus J. M. Smulders,
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45
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Fister AS, Landherr L, Maximova SN, Guiltinan MJ. Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao. FRONTIERS IN PLANT SCIENCE 2018; 9:268. [PMID: 29552023 PMCID: PMC5841092 DOI: 10.3389/fpls.2018.00268] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/14/2018] [Indexed: 05/19/2023]
Abstract
Theobroma cacao, the source of cocoa, suffers significant losses to a variety of pathogens resulting in reduced incomes for millions of farmers in developing countries. Development of disease resistant cacao varieties is an essential strategy to combat this threat, but is limited by sources of genetic resistance and the slow generation time of this tropical tree crop. In this study, we present the first application of genome editing technology in cacao, using Agrobacterium-mediated transient transformation to introduce CRISPR/Cas9 components into cacao leaves and cotyledon cells. As a first proof of concept, we targeted the cacao Non-Expressor of Pathogenesis-Related 3 (TcNPR3) gene, a suppressor of the defense response. After demonstrating activity of designed single-guide RNAs (sgRNA) in vitro, we used Agrobacterium to introduce a CRISPR/Cas9 system into leaf tissue, and identified the presence of deletions in 27% of TcNPR3 copies in the treated tissues. The edited tissue exhibited an increased resistance to infection with the cacao pathogen Phytophthora tropicalis and elevated expression of downstream defense genes. Analysis of off-target mutagenesis in sequences similar to sgRNA target sites using high-throughput sequencing did not reveal mutations above background sequencing error rates. These results confirm the function of NPR3 as a repressor of the cacao immune system and demonstrate the application of CRISPR/Cas9 as a powerful functional genomics tool for cacao. Several stably transformed and genome edited somatic embryos were obtained via Agrobacterium-mediated transformation, and ongoing work will test the effectiveness of this approach at a whole plant level.
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Affiliation(s)
- Andrew S. Fister
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
| | - Lena Landherr
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
| | - Siela N. Maximova
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Mark J. Guiltinan
- Department of Plant Science, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Mark J. Guiltinan
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Scheben A, Wolter F, Batley J, Puchta H, Edwards D. Towards CRISPR/Cas crops - bringing together genomics and genome editing. THE NEW PHYTOLOGIST 2017; 216:682-698. [PMID: 28762506 DOI: 10.1111/nph.14702] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/31/2017] [Indexed: 05/19/2023]
Abstract
Contents 682 I. 682 II. 683 III. 684 IV. 685 V. 685 VI. 688 VII. 690 VIII. 694 694 References 694 SUMMARY: With the rapid increase in the global population and the impact of climate change on agriculture, there is a need for crops with higher yields and greater tolerance to abiotic stress. However, traditional crop improvement via genetic recombination or random mutagenesis is a laborious process and cannot keep pace with increasing crop demand. Genome editing technologies such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) allow targeted modification of almost any crop genome sequence to generate novel variation and accelerate breeding efforts. We expect a gradual shift in crop improvement away from traditional breeding towards cycles of targeted genome editing. Crop improvement using genome editing is not constrained by limited existing variation or the requirement to select alleles over multiple breeding generations. However, current applications of crop genome editing are limited by the lack of complete reference genomes, the sparse knowledge of potential modification targets, and the unclear legal status of edited crops. We argue that overcoming technical and social barriers to the application of genome editing will allow this technology to produce a new generation of high-yielding, climate ready crops.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Felix Wolter
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
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Yadav R, Kumar V, Baweja M, Shukla P. Gene editing and genetic engineering approaches for advanced probiotics: A review. Crit Rev Food Sci Nutr 2017; 58:1735-1746. [PMID: 28071925 DOI: 10.1080/10408398.2016.1274877] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance. The genetic manipulation of probiotic microorganisms is crucial for defining their role in intestinal microbiota and exploring their beneficial properties. This review describes an overview of gene editing and systems biology approaches, highlighting the advent of omics methods which allows the study of new routes for studying probiotic bacteria. We have also summarized gene editing tools like TALEN, ZFNs and CRISPR-Cas that edits or cleave the specific target DNA. Furthermore, in this review an overview of proposed design of advanced customized probiotic is also hypothesized to improvise the probiotics.
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Affiliation(s)
- Ruby Yadav
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Vishal Kumar
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Mehak Baweja
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Pratyoosh Shukla
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
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48
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Mawphlang OIL, Kharshiing EV. Photoreceptor Mediated Plant Growth Responses: Implications for Photoreceptor Engineering toward Improved Performance in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1181. [PMID: 28744290 PMCID: PMC5504655 DOI: 10.3389/fpls.2017.01181] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/20/2017] [Indexed: 05/18/2023]
Abstract
Rising temperatures during growing seasons coupled with altered precipitation rates presents a challenging task of improving crop productivity for overcoming such altered weather patterns and cater to a growing population. Light is a critical environmental factor that exerts a powerful influence on plant growth and development ranging from seed germination to flowering and fruiting. Higher plants utilize a suite of complex photoreceptor proteins to perceive surrounding red/far-red (phytochromes), blue/UV-A (cryptochromes, phototropins, ZTL/FKF1/LKP2), and UV-B light (UVR8). While genomic studies have also shown that light induces extensive reprogramming of gene expression patterns in plants, molecular genetic studies have shown that manipulation of one or more photoreceptors can result in modification of agronomically beneficial traits. Such information can assist researchers to engineer photoreceptors via genome editing technologies to alter expression or even sensitivity thresholds of native photoreceptors for targeting aspects of plant growth that can confer superior agronomic value to the engineered crops. Here we summarize the agronomically important plant growth processes influenced by photoreceptors in crop species, alongwith the functional interactions between different photoreceptors and phytohormones in regulating these responses. We also discuss the potential utility of synthetic biology approaches in photobiology for improving agronomically beneficial traits of crop plants by engineering designer photoreceptors.
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49
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Aznar-Moreno JA, Durrett TP. Simultaneous Targeting of Multiple Gene Homeologs to Alter Seed Oil Production in Camelina sativa. PLANT & CELL PHYSIOLOGY 2017; 58:1260-1267. [PMID: 28444368 DOI: 10.1093/pcp/pcx058] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/14/2017] [Indexed: 05/20/2023]
Abstract
The ability to transform Camelina sativa easily with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologs can code for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways. New genome editing technologies, such as that offered by the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system, offer the capability to introduce mutations into specifically targeted genomic sites. Here, by using a carefully designed guide RNA identical to all three homeologs, we demonstrate the ability of the CRISPR/Cas genome editing system to introduce mutations in all three CsDGAT1 or CsPDAT1 homeologous genes important for triacylglycerol (TAG) synthesis in developing seeds. Sequence analysis from transgenic T1 plants revealed that each CsDGAT1 or each CsPDAT1 homeolog was altered by multiple mutations, resulting in a genetic mosaic in the plants. Interestingly, seed harvested from both CsDGAT1- and CsPDAT1-targeted lines was often shrunken and wrinkled. Further, lipid analysis revealed that many lines produced seed with reduced oil content and altered fatty acid composition, consistent with the role of the targeted genes in seed oil biosynthesis. The CRISPR/Cas system therefore represents a useful method to alter endogenous biosynthetic pathways efficiently in polyploid species such as camelina.
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Affiliation(s)
- J A Aznar-Moreno
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - T P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
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AKBUDAK MA, KONTBAY K. Yeni Nesil Genom Düzenleme Teknikleri: ZFN, TALEN, CRISPR’lar ve Bitkilerde Kullanımı. ACTA ACUST UNITED AC 2017. [DOI: 10.21566/tarbitderg.323614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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