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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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52
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Xie Y, Liu Y, Wang H, Ma X, Wang B, Wu G, Wang H. Phytochrome-interacting factors directly suppress MIR156 expression to enhance shade-avoidance syndrome in Arabidopsis. Nat Commun 2017; 8:348. [PMID: 28839125 PMCID: PMC5570905 DOI: 10.1038/s41467-017-00404-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/24/2017] [Indexed: 12/22/2022] Open
Abstract
Plants have evolved a repertoire of strategies collectively termed the shade-avoidance syndrome to avoid shade from canopy and compete for light with their neighbors. However, the signaling mechanism governing the adaptive changes of adult plant architecture to shade is not well understood. Here, we show that in Arabidopsis, compared with the wild type, several PHYTOCHROME-INTERACTING FACTORS (PIFS) overexpressors all display constitutive shade-avoidance syndrome under normal high red to far-red light ratio conditions but are less sensitive to the simulated shade, whereas the MIR156 overexpressors exhibit an opposite phenotype. The simulated shade induces rapid accumulation of PIF proteins, reduced expression of multiple MIR156 genes, and concomitant elevated expression of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family genes. Moreover, in vivo and in vitro assays indicate that PIFs bind to the promoters of several MIR156 genes directly and repress their expression. Our results establish a direct functional link between the phytochrome-PIFs and miR156-SPL regulatory modules in mediating shade-avoidance syndrome.Plants employ developmental strategies to avoid shade and compete with neighbors for light. Here, Xie et al. show that phytochrome-interacting factors, which are regulated in a light-dependent manner, directly repress MIR156 genes and promote the expression of SPL genes to enhance shade-avoidance responses.
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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53
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Yang H, Wu JJ, Tang T, Liu KD, Dai C. CRISPR/Cas9-mediated genome editing efficiently creates specific mutations at multiple loci using one sgRNA in Brassica napus. Sci Rep 2017; 7:7489. [PMID: 28790350 PMCID: PMC5548805 DOI: 10.1038/s41598-017-07871-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
CRISPR/Cas9 is a valuable tool for both basic and applied research that has been widely applied to different plant species. Nonetheless, a systematical assessment of the efficiency of this method is not available for the allotetraploid Brassica napus-an important oilseed crop. In this study, we examined the mutation efficiency of the CRISPR/Cas9 method for 12 genes and also determined the pattern, specificity and heritability of these gene modifications in B. napus. The average mutation frequency for a single-gene targeted sgRNA in the T0 generation is 65.3%. For paralogous genes located in conserved regions that were targeted by sgRNAs, we observed mutation frequencies that ranged from 27.6% to 96.6%. Homozygotes were readily found in T0 plants. A total of 48.2% of the gene mutations, including homozygotes, bi-alleles, and heterozygotes were stably inherited as classic Mendelian alleles in the next generation (T1) without any new mutations or reversions. Moreover, no mutation was found in the putative off-target sites among the examined T0 plants. Collectively, our results demonstrate that CRISPR/Cas9 is an efficient tool for creating targeted genome modifications at multiple loci that are stable and inheritable in B. napus. These findings open many doors for biotechnological applications in oilseed crops.
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Affiliation(s)
- Hong Yang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia-Jing Wu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ting Tang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ke-De Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Cheng Dai
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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54
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Liu X, Xie C, Si H, Yang J. CRISPR/Cas9-mediated genome editing in plants. Methods 2017; 121-122:94-102. [PMID: 28315486 DOI: 10.1016/j.ymeth.2017.03.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 01/09/2023] Open
Abstract
The increasing burden of the world's population on agriculture necessitates the development of more robust crops. As the amount of information from sequenced crop genomes increases, technology can be used to investigate the function of genes in detail and to design improved crops at the molecular level. Recently, an RNA-programmed genome-editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9 has provided a powerful platform to achieve these goals. By combining versatile tools to study and modify plants at different molecular levels, the CRISPR/Cas9 system is paving the way towards a new horizon for basic research and crop development. In this review, the accomplishments, problems and improvements of this technology in plants, including target sequence cleavage, knock-in/gene replacement, transcriptional regulation, epigenetic modification, off-target effects, delivery system and potential applications, will be highlighted.
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Affiliation(s)
- Xuejun Liu
- TianJin Crops Research Institute, China.
| | - Chuanxiao Xie
- Institute of Crop Science of Chinese Academy of Agricultural Sciences, China.
| | - Huaijun Si
- College of Life Science and Technology, GanSu Agricultural University, China.
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55
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Wang Y, Meng Z, Liang C, Meng Z, Wang Y, Sun G, Zhu T, Cai Y, Guo S, Zhang R, Lin Y. Increased lateral root formation by CRISPR/Cas9-mediated editing of arginase genes in cotton. SCIENCE CHINA. LIFE SCIENCES 2017; 60:524-527. [PMID: 28527115 DOI: 10.1007/s11427-017-9031-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/09/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Yanling Wang
- School of Life Science, Anhui Agricultural University, Hefei, 230061, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaohong Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, 230061, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, 230061, China.
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56
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Li MW, Xin D, Gao Y, Li KP, Fan K, Muñoz NB, Yung WS, Lam HM. Using genomic information to improve soybean adaptability to climate change. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1823-1834. [PMID: 27660480 DOI: 10.1093/jxb/erw348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield - including that of soybean - due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.
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Affiliation(s)
- Man-Wah Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Dawei Xin
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yishu Gao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kwan-Pok Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kejing Fan
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Nacira Belen Muñoz
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Wai-Shing Yung
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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Abstract
The plant-specific RING-domain finger proteins play important roles in plant development and stress responses. We recently identified and functionally characterized a stress-induced gene OsSRFP1 (Oryza sativa Stress-related RING Finger Protein 1) from rice. We showed evidences of the biotechnological potential of the suppression of OsSRFP1 expression in conferring cold tolerance. The increased cold tolerance of OsSRFP1 knock-down plants was associated with higher amounts of free proline and activities of antioxidant enzymes. In vitro ubiquitination assays showed that OsSRFP1 possessed E3 ubiquitin ligase activity. Some predicted interacting partners of OsSRFP1 might be the substrates for OsSRFP1-mediated protein degradation. Interestingly, OsSRFP1 had trans-activation activity, suggesting the dual roles of OsSRFP1 in post-translational and transcriptional regulations in stress responses.
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Affiliation(s)
- Huimin Fang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing , China
| | - Qingling Meng
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing , China
| | - Hongsheng Zhang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing , China
| | - Ji Huang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing , China
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58
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Bortesi L, Zhu C, Zischewski J, Perez L, Bassié L, Nadi R, Forni G, Lade SB, Soto E, Jin X, Medina V, Villorbina G, Muñoz P, Farré G, Fischer R, Twyman RM, Capell T, Christou P, Schillberg S. Patterns of CRISPR/Cas9 activity in plants, animals and microbes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2203-2216. [PMID: 27614091 PMCID: PMC5103219 DOI: 10.1111/pbi.12634] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 05/19/2023]
Abstract
The CRISPR/Cas9 system and related RNA-guided endonucleases can introduce double-strand breaks (DSBs) at specific sites in the genome, allowing the generation of targeted mutations in one or more genes as well as more complex genomic rearrangements. Modifications of the canonical CRISPR/Cas9 system from Streptococcus pyogenes and the introduction of related systems from other bacteria have increased the diversity of genomic sites that can be targeted, providing greater control over the resolution of DSBs, the targeting efficiency (frequency of on-target mutations), the targeting accuracy (likelihood of off-target mutations) and the type of mutations that are induced. Although much is now known about the principles of CRISPR/Cas9 genome editing, the likelihood of different outcomes is species-dependent and there have been few comparative studies looking at the basis of such diversity. Here we critically analyse the activity of CRISPR/Cas9 and related systems in different plant species and compare the outcomes in animals and microbes to draw broad conclusions about the design principles required for effective genome editing in different organisms. These principles will be important for the commercial development of crops, farm animals, animal disease models and novel microbial strains using CRISPR/Cas9 and other genome-editing tools.
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Affiliation(s)
- Luisa Bortesi
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Changfu Zhu
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Julia Zischewski
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Lucia Perez
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Ludovic Bassié
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Riad Nadi
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Giobbe Forni
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Sarah Boyd Lade
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Erika Soto
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Xin Jin
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Vicente Medina
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Gemma Villorbina
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Pilar Muñoz
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Gemma Farré
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Rainer Fischer
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | | | - Teresa Capell
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
| | - Paul Christou
- Department of Plant Production and Forestry ScienceSchool of Agrifood and Forestry Science and Engineering (ETSEA)University of Lleida‐Agrotecnio CenterLleidaSpain
- ICREACatalan Institute for Research and Advanced StudiesBarcelonaSpain
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
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59
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Ren C, Liu X, Zhang Z, Wang Y, Duan W, Li S, Liang Z. CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Sci Rep 2016; 6:32289. [PMID: 27576893 PMCID: PMC5006071 DOI: 10.1038/srep32289] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/04/2016] [Indexed: 12/21/2022] Open
Abstract
The type II clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 system (CRISPR/Cas9) has been successfully applied to edit target genes in multiple plant species. However, it remains unknown whether this system can be used for genome editing in grape. In this study, we described genome editing and targeted gene mutation in ‘Chardonnay’ suspension cells and plants via the CRISPR/Cas9 system. Two single guide RNAs (sgRNAs) were designed to target distinct sites of the L-idonate dehydrogenase gene (IdnDH). CEL I endonuclease assay and sequencing results revealed the expected indel mutations at the target site, and a mutation frequency of 100% was observed in the transgenic cell mass (CM) as well as corresponding regenerated plants with expression of sgRNA1/Cas9. The majority of the detected mutations in transgenic CM were 1-bp insertions, followed by 1- to 3-nucleotide deletions. Off-target activities were also evaluated by sequencing the potential off-target sites, and no obvious off-target events were detected. Our results demonstrated that the CRISPR/Cas9 system is an efficient and specific tool for precise genome editing in grape.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhan Zhang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, PR China
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60
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Turina M, Kormelink R, Resende RO. Resistance to Tospoviruses in Vegetable Crops: Epidemiological and Molecular Aspects. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:347-371. [PMID: 27296139 DOI: 10.1146/annurev-phyto-080615-095843] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
During the past three decades, the economic impact of tospoviruses has increased, causing high yield losses in a variety of crops and ornamentals. Owing to the difficulty in combating thrips vectors with insecticides, the best way to limit/prevent tospovirus-induced diseases involves a management strategy that includes virus resistance. This review briefly presents current tospovirus taxonomy, diversity, molecular biology, and cytopathology as an introduction to a more extensive description of the two main resistance genes employed against tospoviruses: the Sw5 gene in tomato and the Tsw in pepper. Natural and experimental resistance-breaking (RB) isolates allowed the identification of the viral avirulence protein triggering each of the two resistance gene products; epidemiology of RB isolates is discussed to reinforce the need for allelic variants and the need to search for new/alternative resistance genes. Ongoing efforts for alternative resistance strategies are described not only for Tomato spotted wilt virus (TSWV) in pepper and tomato but also for other vegetable crops heavily impacted by tospoviruses.
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Affiliation(s)
- Massimo Turina
- Institute for Sustainable Plant Protection, CNR Torino, 10135 Torino, Italy;
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Renato O Resende
- Department of Cell Biology, University of Brasília, 70910-900 Brasília, DF, Brazil
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61
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Yu B, Lu R, Yuan Y, Zhang T, Song S, Qi Z, Shao B, Zhu M, Mi F, Cheng Y. Efficient TALEN-mediated myostatin gene editing in goats. BMC DEVELOPMENTAL BIOLOGY 2016; 16:26. [PMID: 27461387 PMCID: PMC4962387 DOI: 10.1186/s12861-016-0126-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Background Myostatin (MSTN) encodes a negative regulator of skeletal muscle mass that might have applications for promoting muscle growth in livestock. In this study, we aimed to test whether targeted MSTN editing, mediated by transcription activator-like effector nucleases (TALENs), is a viable approach to create myostatin-modified goats (Capra hircus). Results We obtained a pair of TALENs (MTAL-2) that could recognize and cut the targeted MSTN site in the goat genome. Fibroblasts from pedigreed goats were co-transfected with MTAL-2, and 272 monoclonal cell strains were confirmed to have mono- or bi-allelic mutations in MSTN. Ten cell strains with different genotypes were used as donor cells for somatic cell nuclear transfer, which produced three cloned kids (K179/MSTN−/−, K52-2/MSTN+/−, and K52-1/MSTN+/+). Conclusions The results suggested that the MTAL-2 could disrupt MSTN efficiently in the goat genome. The mutated somatic cells could be used to produce MSTN-site mutated goats without developmental disruption. Thus, TALENs is an effective method for accurate genome editing to produce site-modified goats. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0126-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Baoli Yu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Rui Lu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Yuguo Yuan
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Ting Zhang
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Shaozheng Song
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Zhengqiang Qi
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Bin Shao
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Mengmin Zhu
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Fei Mi
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Yong Cheng
- College of Veterinary Medicine, Yangzhou University, No. 12 Wenhui Road, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
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Cardi T, Neal Stewart C. Progress of targeted genome modification approaches in higher plants. PLANT CELL REPORTS 2016; 35:1401-16. [PMID: 27025856 DOI: 10.1007/s00299-016-1975-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 05/07/2023]
Abstract
Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.
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Affiliation(s)
- Teodoro Cardi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Centro di Ricerca per l'Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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63
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Schaeffer SM, Nakata PA. The expanding footprint of CRISPR/Cas9 in the plant sciences. PLANT CELL REPORTS 2016; 35:1451-68. [PMID: 27137209 DOI: 10.1007/s00299-016-1987-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 has evolved and transformed the field of biology at an unprecedented pace. From the initial purpose of introducing a site specific mutation within a genome of choice, this technology has morphed into enabling a wide array of molecular applications, including site-specific transgene insertion and multiplexing for the simultaneous induction of multiple cleavage events. Efficiency, specificity, and flexibility are key attributes that have solidified CRISPR/Cas9 as the genome-editing tool of choice by scientists from all areas of biology. Within the field of plant biology, several CRISPR/Cas9 technologies, developed in other biological systems, have been successfully implemented to probe plant gene function and to modify specific crop traits. It is anticipated that this trend will persist and lead to the development of new applications and modifications of the CRISPR technology, adding to an ever-expanding collection of genome-editing tools. We envision that these tools will bestow plant researchers with new utilities to alter genome complexity, engineer site-specific integration events, control gene expression, generate transgene-free edited crops, and prevent or cure plant viral disease. The successful implementation of such utilities will represent a new frontier in plant biotechnology.
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Affiliation(s)
- Scott M Schaeffer
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Houston, TX, 77030-2600, USA
| | - Paul A Nakata
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Houston, TX, 77030-2600, USA.
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64
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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Khatodia S, Bhatotia K, Passricha N, Khurana SMP, Tuteja N. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops. FRONTIERS IN PLANT SCIENCE 2016; 7:506. [PMID: 27148329 PMCID: PMC4835450 DOI: 10.3389/fpls.2016.00506] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2016] [Indexed: 05/18/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses.
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Affiliation(s)
- Surender Khatodia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Kirti Bhatotia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - S. M. P. Khurana
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
- Amity Institute of Microbial Technology, Amity UniversityNoida, India
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Exploiting the CRISPR/Cas9 System for Targeted Genome Mutagenesis in Petunia. Sci Rep 2016; 6:20315. [PMID: 26837606 PMCID: PMC4738242 DOI: 10.1038/srep20315] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/30/2015] [Indexed: 12/23/2022] Open
Abstract
Recently, CRISPR/Cas9 technology has emerged as a powerful approach for targeted genome modification in eukaryotic organisms from yeast to human cell lines. Its successful application in several plant species promises enormous potential for basic and applied plant research. However, extensive studies are still needed to assess this system in other important plant species, to broaden its fields of application and to improve methods. Here we showed that the CRISPR/Cas9 system is efficient in petunia (Petunia hybrid), an important ornamental plant and a model for comparative research. When PDS was used as target gene, transgenic shoot lines with albino phenotype accounted for 55.6%–87.5% of the total regenerated T0 Basta-resistant lines. A homozygous deletion close to 1 kb in length can be readily generated and identified in the first generation. A sequential transformation strategy—introducing Cas9 and sgRNA expression cassettes sequentially into petunia—can be used to make targeted mutations with short indels or chromosomal fragment deletions. Our results present a new plant species amenable to CRIPR/Cas9 technology and provide an alternative procedure for its exploitation.
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Abstract
The cytokinins have been implicated in many facets of plant growth and development including cell division and differentiation, shoot and root growth, apical dominance, senescence, fruit and seed development, and the response to biotic and abiotic stressors. Cytokinin levels are regulated by a balance between biosynthesis [isopentenyl transferase (IPT)], activation [Lonely Guy (LOG)], inactivation (O-glucosyl transferase), re-activation (β-glucosidase), and degradation [cytokinin oxidase/dehydrogenase (CKX)]. During senescence, the levels of active cytokinins decrease, with premature senescence leading to a decrease in yield. During the early stages of fruit and seed development, cytokinin levels are transiently elevated, and coincide with nuclear and cell divisions which are a determinant of final seed size. Exogenous application of cytokinin, ectopic expression of IPT, or down-regulation of CKX have, on occasions, led to increased seed yield, leading to the suggestion that cytokinin may be limiting yield. However, manipulation of cytokinins is complex, not only because of their pleiotropic nature but also because the genes coding for biosynthesis and metabolism belong to multigene families, the members of which are themselves spatially and temporally differentiated. Previous research on yield of rice showed that plant breeders could directly target the cytokinins. Modern genome editing tools could be employed to target and manipulate cytokinin levels to increase seed yield with the concurrent aim of maintaining quality. However, how the cytokinin level is modified and whether IPT or CKX is targeted may depend on whether the plant is considered to be in a source-limiting environment or to be sink limited.
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Affiliation(s)
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand School of Life Sciences, Yantai University, Yantai 264005, China
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68
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Schaeffer SM, Nakata PA. CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:130-42. [PMID: 26475194 DOI: 10.1016/j.plantsci.2015.09.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 05/22/2023]
Abstract
The CRISPR/Cas9 genome engineering system has ignited and swept through the scientific community like wildfire. Owing largely to its efficiency, specificity, and flexibility, the CRISPR/Cas9 system has quickly become the preferred genome-editing tool of plant scientists. In plants, much of the early CRISPR/Cas9 work has been limited to proof of concept and functional studies in model systems. These studies, along with those in other fields of biology, have led to the development of several utilities of CRISPR/Cas9 beyond single gene editing. Such utilities include multiplexing for inducing multiple cleavage events, controlling gene expression, and site specific transgene insertion. With much of the conceptual CRISPR/Cas9 work nearly complete, plant researchers are beginning to apply this gene editing technology for crop trait improvement. Before rational strategies can be designed to implement this technology to engineer a wide array of crops there is a need to expand the availability of crop-specific vectors, genome resources, and transformation protocols. We anticipate that these challenges will be met along with the continued evolution of the CRISPR/Cas9 system particularly in the areas of manipulation of large genomic regions, transgene-free genetic modification, development of breeding resources, discovery of gene function, and improvements upon CRISPR/Cas9 components. The CRISPR/Cas9 editing system appears poised to transform crop trait improvement.
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Affiliation(s)
- Scott M Schaeffer
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2600, United States
| | - Paul A Nakata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2600, United States.
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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70
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Sun X, Hu Z, Chen R, Jiang Q, Song G, Zhang H, Xi Y. Targeted mutagenesis in soybean using the CRISPR-Cas9 system. Sci Rep 2015; 5:10342. [PMID: 26022141 PMCID: PMC4448504 DOI: 10.1038/srep10342] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
Genome editing is a valuable technique for gene function analysis and crop improvement. Over the past two years, the CRISPR-Cas9 system has emerged as a powerful tool for precisely targeted gene editing. In this study, we predicted 11 U6 genes in soybean (Glycine max L.). We then constructed two vectors (pCas9-GmU6-sgRNA and pCas9-AtU6-sgRNA) using the soybean U6-10 and Arabidopsis U6-26 promoters, respectively, to produce synthetic guide RNAs (sgRNAs) for targeted gene mutagenesis. Three genes, Glyma06g14180, Glyma08g02290 and Glyma12g37050, were selected as targets. Mutations of these three genes were detected in soybean protoplasts. The vectors were then transformed into soybean hairy roots by Agrobacterium rhizogenes infection, resulting in efficient target gene editing. Mutation efficiencies ranged from 3.2-9.7% using the pCas9-AtU6-sgRNA vector and 14.7-20.2% with the pCas9-GmU6-sgRNA vector. Biallelic mutations in Glyma06g14180 and Glyma08g02290 were detected in transgenic hairy roots. Off-target activities associated with Glyma06g14180 and Glyma12g37050 were also detected. Off-target activity would improve mutation efficiency for the construction of a saturated gene mutation library in soybean. Targeted mutagenesis using the CRISPR-Cas9 system should advance soybean functional genomic research, especially that of genes involved in the roots and nodules.
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Affiliation(s)
- Xianjun Sun
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zheng Hu
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Qiyang Jiang
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guohua Song
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hui Zhang
- National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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71
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Rajendran SRCK, Yau YY, Pandey D, Kumar A. CRISPR-Cas9 Based Genome Engineering: Opportunities in Agri-Food-Nutrition and Healthcare. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:261-75. [PMID: 25871888 DOI: 10.1089/omi.2015.0023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently developed strategies and techniques that make use of the vast amount of genetic information to perform targeted perturbations in the genome of living organisms are collectively referred to as genome engineering. The wide array of applications made possible by the use of this technology range from agriculture to healthcare. This, along with the applications involving basic biological research, has made it a very dynamic and active field of research. This review focuses on the CRISPR system from its discovery and role in bacterial adaptive immunity to the most recent developments, and its possible applications in agriculture and modern medicine.
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Affiliation(s)
- Subin Raj Cheri Kunnumal Rajendran
- 1 Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology , Pantnagar, U.S. Nagar, Uttarakhand, India
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Palmgren MG, Edenbrandt AK, Vedel SE, Andersen MM, Landes X, Østerberg JT, Falhof J, Olsen LI, Christensen SB, Sandøe P, Gamborg C, Kappel K, Thorsen BJ, Pagh P. Are we ready for back-to-nature crop breeding? TRENDS IN PLANT SCIENCE 2015; 20:155-64. [PMID: 25529373 DOI: 10.1016/j.tplants.2014.11.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/05/2014] [Accepted: 11/10/2014] [Indexed: 05/03/2023]
Abstract
Sustainable agriculture in response to increasing demands for food depends on development of high-yielding crops with high nutritional value that require minimal intervention during growth. To date, the focus has been on changing plants by introducing genes that impart new properties, which the plants and their ancestors never possessed. By contrast, we suggest another potentially beneficial and perhaps less controversial strategy that modern plant biotechnology may adopt. This approach, which broadens earlier approaches to reverse breeding, aims to furnish crops with lost properties that their ancestors once possessed in order to tolerate adverse environmental conditions. What molecular techniques are available for implementing such rewilding? Are the strategies legally, socially, economically, and ethically feasible? These are the questions addressed in this review.
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Affiliation(s)
- Michael G Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Anna Kristina Edenbrandt
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
| | - Suzanne Elizabeth Vedel
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
| | - Martin Marchman Andersen
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, DK-2300 Copenhagen S, Denmark
| | - Xavier Landes
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, DK-2300 Copenhagen S, Denmark
| | - Jeppe Thulin Østerberg
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Janus Falhof
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Lene Irene Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Søren Brøgger Christensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Peter Sandøe
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark; Department of Large Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Christian Gamborg
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
| | - Klemens Kappel
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, DK-2300 Copenhagen S, Denmark
| | - Bo Jellesmark Thorsen
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
| | - Peter Pagh
- Centre for Public Regulation and Administration, Faculty of Law, University of Copenhagen, Studiestræde 6, DK-1455 Copenhagen K, Denmark
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73
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Coffman VC, Wu JQ. Every laboratory with a fluorescence microscope should consider counting molecules. Mol Biol Cell 2015; 25:1545-8. [PMID: 24825827 PMCID: PMC4019486 DOI: 10.1091/mbc.e13-05-0249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Protein numbers in cells determine rates of biological processes, influence the architecture of cellular structures, reveal the stoichiometries of protein complexes, guide in vitro biochemical reconstitutions, and provide parameter values for mathematical modeling. The purpose of this essay is to increase awareness of methods for counting protein molecules using fluorescence microscopy and encourage more cell biologists to report these numbers. We address the state of the field in terms of utility and accuracy of the numbers reported and point readers to references for details of specific techniques and applications.
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Affiliation(s)
- Valerie C Coffman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Jian-Qiu Wu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210
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74
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Kalluri UC, Yin H, Yang X, Davison BH. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1207-16. [PMID: 25363806 PMCID: PMC4265275 DOI: 10.1111/pbi.12283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 05/19/2023]
Abstract
Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.
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Affiliation(s)
- Udaya C Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- * Correspondence (Tel 1 865 576 9495, fax 1 865 576 9939; email )
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Brian H Davison
- BioEnergy Science Center and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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Acevedo-Garcia J, Kusch S, Panstruga R. Magical mystery tour: MLO proteins in plant immunity and beyond. THE NEW PHYTOLOGIST 2014; 204:273-81. [PMID: 25453131 DOI: 10.1111/nph.12889] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Stable heritable restriction of the ubiquitous powdery mildew disease is a desirable trait for agri and horticulture. In barley (Hordeum vulgare), loss-of-function mutant alleles of the Mildew resistance locus o (Mlo) gene confer broad-spectrum resistance to almost all known isolates of the fungal barley powdery mildew pathogen, Blumeria graminis f.sp. hordei. Despite extensive cultivation of barley mlo genotypes, mlo resistance has been durable in the field. Mlo genes are present as small families in the genomes of all higher plant species. The presumed negative regulatory role of particular members in plant immunity is evolutionarily conserved, as powdery mildew resistant mlo mutants have also been described in Arabidopsis thaliana, tomato(Solanum lycopersicum) and pea (Pisum sativum). Barley Mlo encodes a plasma membrane-localized seven-transmembrane domain protein of unknown biochemical activity. Here, we review the known requirements for mlo-mediated disease resistance in barley and Arabidopsis and reflect current views regarding Mlo function. We discuss additional mlo mutant phenotypes recently discovered in Arabidopsis and present a meta-analysis of the phylogenetic relationships within the Mlo family. Finally, we consider the novel versatile tools for functional analysis and targeted genome modification that can be used to induce mlo-based powdery mildew resistance in virtually any plant species.
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Affiliation(s)
- Johanna Acevedo-Garcia
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
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Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:797-807. [PMID: 24854982 DOI: 10.1111/pbi.12200] [Citation(s) in RCA: 481] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/14/2014] [Accepted: 04/16/2014] [Indexed: 05/18/2023]
Abstract
The CRISPR/Cas9 system has been demonstrated to efficiently induce targeted gene editing in a variety of organisms including plants. Recent work showed that CRISPR/Cas9-induced gene mutations in Arabidopsis were mostly somatic mutations in the early generation, although some mutations could be stably inherited in later generations. However, it remains unclear whether this system will work similarly in crops such as rice. In this study, we tested in two rice subspecies 11 target genes for their amenability to CRISPR/Cas9-induced editing and determined the patterns, specificity and heritability of the gene modifications. Analysis of the genotypes and frequency of edited genes in the first generation of transformed plants (T0) showed that the CRISPR/Cas9 system was highly efficient in rice, with target genes edited in nearly half of the transformed embryogenic cells before their first cell division. Homozygotes of edited target genes were readily found in T0 plants. The gene mutations were passed to the next generation (T1) following classic Mendelian law, without any detectable new mutation or reversion. Even with extensive searches including whole genome resequencing, we could not find any evidence of large-scale off-targeting in rice for any of the many targets tested in this study. By specifically sequencing the putative off-target sites of a large number of T0 plants, low-frequency mutations were found in only one off-target site where the sequence had 1-bp difference from the intended target. Overall, the data in this study point to the CRISPR/Cas9 system being a powerful tool in crop genome engineering.
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Affiliation(s)
- Hui Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
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Nakashima N, Miyazaki K. Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci 2014; 15:2773-93. [PMID: 24552876 PMCID: PMC3958881 DOI: 10.3390/ijms15022773] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/18/2022] Open
Abstract
Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.
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Affiliation(s)
- Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
| | - Kentaro Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Abstract
To confer resistance against pathogens and pests in plants, typically dominant resistance genes are deployed. However, because resistance is based on recognition of a single pathogen-derived molecular pattern, these narrow-spectrum genes are usually readily overcome. Disease arises from a compatible interaction between plant and pathogen. Hence, altering a plant gene that critically facilitates compatibility could provide a more broad-spectrum and durable type of resistance. Here, such susceptibility (S) genes are reviewed with a focus on the mechanisms underlying loss of compatibility. We distinguish three groups of S genes acting during different stages of infection: early pathogen establishment, modulation of host defenses, and pathogen sustenance. The many examples reviewed here show that S genes have the potential to be used in resistance breeding. However, because S genes have a function other than being a compatibility factor for the pathogen, the side effects caused by their mutation demands a one-by-one assessment of their usefulness for application.
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