1
|
Tanveer M, Abidin ZU, Alawadi HFN, Shahzad AN, Mahmood A, Khan BA, Qari S, Oraby HF. Recent advances in genome editing strategies for balancing growth and defence in sugarcane ( Saccharum officinarum). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24036. [PMID: 38696670 DOI: 10.1071/fp24036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/14/2024] [Indexed: 05/04/2024]
Abstract
Sugarcane (Saccharum officinarum ) has gained more attention worldwide in recent decades because of its importance as a bioenergy resource and in producing table sugar. However, the production capabilities of conventional varieties are being challenged by the changing climates, which struggle to meet the escalating demands of the growing global population. Genome editing has emerged as a pivotal field that offers groundbreaking solutions in agriculture and beyond. It includes inserting, removing or replacing DNA in an organism's genome. Various approaches are employed to enhance crop yields and resilience in harsh climates. These techniques include zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/associated protein (CRISPR/Cas). Among these, CRISPR/Cas is one of the most promising and rapidly advancing fields. With the help of these techniques, several crops like rice (Oryza sativa ), tomato (Solanum lycopersicum ), maize (Zea mays ), barley (Hordeum vulgare ) and sugarcane have been improved to be resistant to viral diseases. This review describes recent advances in genome editing with a particular focus on sugarcane and focuses on the advantages and limitations of these approaches while also considering the regulatory and ethical implications across different countries. It also offers insights into future prospects and the application of these approaches in agriculture.
Collapse
Affiliation(s)
- Maira Tanveer
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Zain Ul Abidin
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | | | - Ahmad Naeem Shahzad
- Department of Agronomy, Bahauddin Zakarriya University, Multan 60650, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Bilal Ahmad Khan
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Sameer Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hesham Farouk Oraby
- Deanship of Scientific Research, Umm Al-Qura University, Makkah 21955, Saudi Arabia; and Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
| |
Collapse
|
2
|
Oberemok V, Laikova K, Golovkin I, Kryukov L, Kamenetsky-Goldstein R. Biotechnology of virus eradication and plant vaccination in phytobiome context. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:3-8. [PMID: 34569131 DOI: 10.1111/plb.13338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.
Collapse
Affiliation(s)
- V Oberemok
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Nikita Botanical Gardens - National Scientific Centre Russian Academy of Sciences, Yalta, Russia
| | - K Laikova
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Research Institute of Agriculture of Crimea, Simferopol, Russia
| | - I Golovkin
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
| | - L Kryukov
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Lobachevsky State University of Nizhni Novgorod, Nizhni Novgorod, Russia
| | | |
Collapse
|
3
|
Fonseca PLC, Mucherino M JJ, Porto JAM, Armache JN, de Almeida JPP, da Silva FF, Olmo RP, Faria IJDS, de Carvalho DS, Góes-Neto A, Corrêa RX, Pirovani CP, Pacheco LGC, Costa MA, Aguiar ERGR. Genome-wide identification of miRNAs and target regulatory network in the invasive ectoparasitic mite Varroa destructor. Genomics 2021; 113:2290-2303. [PMID: 34044154 DOI: 10.1016/j.ygeno.2021.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/29/2022]
Abstract
Varroa destructor is an ectoparasite mite that attacks bees leading to colony disorders worldwide. microRNAs (miRNAs) are key molecules used by eukaryotes to post-transcriptional control of gene expression. Nevertheless, still lack information aboutV. destructor miRNAs and its regulatory networks. Here, we used an integrative strategy to characterize the miRNAs in the V. destructor mite. We identified 310 precursors that give rise to 500 mature miRNAs, which 257 are likely mite-specific elements. miRNAs showed canonical length ranging between 18 and 25 nucleotides and 5' uracil preference. Top 10 elements concentrated over 80% of total miRNA expression, with bantam alone representing ~50%. We also detected non-templated bases in precursor-derived small RNAs, indicative of miRNA post-transcriptional regulatory mechanisms. Finally, we note that conserved miRNAs control similar processes in different organisms, suggesting a conservative role. Altogether, our findings contribute to the better understanding of the mite biology that can assist future studies on varroosis control.
Collapse
Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Jonathan J Mucherino M
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil; Department of Forest Management, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Mérida 5101, Venezuela
| | - Joel A M Porto
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Juliana N Armache
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - João Paulo P de Almeida
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Felipe F da Silva
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, Inserm, Strasbourg, France
| | - Isaque J da S Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Daniel S de Carvalho
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil; Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Ronan X Corrêa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Carlos P Pirovani
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Marco Antônio Costa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms. PLANTS 2019; 8:plants8120575. [PMID: 31817560 PMCID: PMC6963434 DOI: 10.3390/plants8120575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.
Collapse
|
6
|
Miroshnichenko DN, Shulga OA, Timerbaev VR, Dolgov SV. Achievements, Challenges, and Prospects in the Production of Nontransgenic, Genome-Edited Plants. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819090047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Burkhanova GF, Sorokan AV, Cherepanova EA, Sarvarova ER, Khairullin RM, Maksimov IV. Endophytic Bacillus bacteria with RNase activity in the resistance of potato plants to viruses. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Viral diseases annually cause significant crop losses and significantly reduce the quality of products, including potatoes, some of the most important crops. Currently, viruses cannot be controlled with chemical pesticides, since known antiviral compounds are teratogenic and hazardous to people’s health. Biocontrol agents based on endophytic microorganisms may be an alternative to them. Many strains of Bacillus produce ribonucleases (RNases). Our laboratory possesses a collection of bacteria that produce various metabolites and have RNase activity. The results showed that the inoculation of potato with B. subtilis 26D and B. thuringiensis increased the grain yield by 32–43 %. In addition, the treatment of potato plants with Bacillus spp. significantly reduced the infection of potato plants with virus M. The prevalence of the disease in potato plants was significantly reduced from 60 % in the control to 18 % (B. subtillis 26D) and 25–33 % (B. thuringiensis) in the inoculated plants. Similarly, the infection index decreased from 14 in the control to 1 in the inoculated plants. The further study of molecular mechanisms related to bacterial induction of plant defense reactions in response to viral infections will lead to a better understanding of stress resistance problems. The endophytic microorganisms studied in this report may become the basis for the creation of biological agents for plant protection.
Collapse
Affiliation(s)
- G. F. Burkhanova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - A. V. Sorokan
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - E. A. Cherepanova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - E. R. Sarvarova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - R. M. Khairullin
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - I. V. Maksimov
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| |
Collapse
|
8
|
Schmitt-Keichinger C. Manipulating Cellular Factors to Combat Viruses: A Case Study From the Plant Eukaryotic Translation Initiation Factors eIF4. Front Microbiol 2019; 10:17. [PMID: 30804892 PMCID: PMC6370628 DOI: 10.3389/fmicb.2019.00017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Genes conferring resistance to plant viruses fall in two categories; the dominant genes that mostly code for proteins with a nucleotide binding site and leucine rich repeats (NBS-LRR), and that directly or indirectly, recognize viral avirulence factors (Avr), and the recessive genes. The latter provide a so-called recessive resistance. They represent roughly half of the known resistance genes and are alleles of genes that play an important role in the virus life cycle. Conversely, all cellular genes critical for the viral infection virtually represent recessive resistance genes. Based on the well-documented case of recessive resistance mediated by eukaryotic translation initiation factors of the 4E/4G family, this review is intended to summarize the possible approaches to control viruses via their host interactors. Classically, resistant crops have been developed through introgression of natural variants of the susceptibility factor from compatible relatives or by random mutagenesis and screening. Transgenic methods have also been applied to engineer improved crops by overexpressing the translation factor either in its natural form or after directed mutagenesis. More recently, innovative approaches like silencing or genome editing have proven their great potential in model and crop plants. The advantages and limits of these different strategies are discussed. This example illustrates the need to identify and characterize more host factors involved in virus multiplication and to assess their application potential in the control of viral diseases.
Collapse
|
9
|
Fonseca PLC, Badotti F, de Oliveira TFP, Fonseca A, Vaz ABM, Tomé LMR, Abrahão JS, Marques JT, Trindade GS, Chaverri P, Aguiar ERGR, Góes-Neto A. Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus. Virol J 2018; 15:184. [PMID: 30477549 PMCID: PMC6258436 DOI: 10.1186/s12985-018-1095-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022] Open
Abstract
Background Hevea brasiliensis is an important commercial crop due to the high quality of the latex it produces; however, little is known about viral infections in this plant. The only virus described to infect H. brasiliensis until now is a Carlavirus, which was described more than 30 years ago. Virus-derived small interfering RNA (vsiRNAs) are the product of the plant’s antiviral defense triggered by dsRNA viral intermediates generated, during the replication cycle. These vsiRNAs are complementar to viral genomes and have been widely used to identify and characterize viruses in plants. Methods In the present study, we investigated the virome of leaf and sapwood samples from native H. brasiliensis trees collected in two geographic areas in the Brazilian Amazon. Small RNA (sRNA) deep sequencing and bioinformatic tools were used to assembly, identify and characterize viral contigs. Subsequently, PCR amplification techniques were performed to experimentally verify the presence of the viral sequences. Finally, the phylogenetic relationship of the putative new virus with related viral genomes was analyzed. Results Our strategy allowed the identification of 32 contigs with high similarity to viral reference genomes, from which 23 exhibited homology to viruses of the Tymoviridae family. The reads showed a predominant size distribution at 21 nt derived from both strands, which was consistent with the vsiRNAs profile. The presence and genome position of the viral contigs were experimentally confirmed using droplet digital PCR amplifications. A 1913 aa long fragment was obtained and used to infer the phylogenetic relationship of the putative new virus, which indicated that it is taxonomically related to the Grapevine fleck virus, genus Maculavirus. The putative new virus was named Hevea brasiliensis virus (HBrV) in reference to its host. Conclusion The methodological strategy applied here proved to be efficient in detecting and confirming the presence of new viral sequences on a ‘very difficult to manage’ sample. This is the second time that viral sequences, that could be ascribed as a putative novel virus, associated to the rubber tree has been identified. Electronic supplementary material The online version of this article (10.1186/s12985-018-1095-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30421-169, Brazil
| | - Tatiana F P de Oliveira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Antônio Fonseca
- LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Aline B M Vaz
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Luiz M R Tomé
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Jônatas S Abrahão
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Giliane S Trindade
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.,Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
| | - Eric R G R Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil. .,Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, BA, ,40110-100, Brazil.
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
| |
Collapse
|
10
|
Tashkandi M, Ali Z, Aljedaani F, Shami A, Mahfouz MM. Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. PLANT SIGNALING & BEHAVIOR 2018; 13:e1525996. [PMID: 30289378 PMCID: PMC6204811 DOI: 10.1080/15592324.2018.1525996] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
Collapse
Affiliation(s)
- Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ashwag Shami
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- College of Science, Biology Department, Kingdom of Saudi Arabia (KSA), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
11
|
Singh B, Kukreja S, Goutam U. Milestones achieved in response to drought stress through reverse genetic approaches. F1000Res 2018; 7:1311. [PMID: 30631439 PMCID: PMC6290974 DOI: 10.12688/f1000research.15606.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
Drought stress is the most important abiotic stress that constrains crop production and reduces yield drastically. The germplasm of most of the cultivated crops possesses numerous unknown drought stress tolerant genes. Moreover, there are many reports suggesting that the wild species of most of the modern cultivars have abiotic stress tolerant genes. Due to climate change and population booms, food security has become a global issue. To develop drought tolerant crop varieties knowledge of various genes involved in drought stress is required. Different reverse genetic approaches such as virus-induced gene silencing (VIGS), clustered regularly interspace short palindromic repeat (CRISPR), targeting induced local lesions in genomes (TILLING) and expressed sequence tags (ESTs) have been used extensively to study the functionality of different genes involved in response to drought stress. In this review, we described the contributions of different techniques of functional genomics in the study of drought tolerant genes.
Collapse
Affiliation(s)
- Baljeet Singh
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sarvjeet Kukreja
- Department of Botany, Ch. MRM Memorial College, Sriganganagar, Rajasthan, 335804, India
| | - Umesh Goutam
- Biotechnology, Lovely Professional University, Phagwara, Punjab, 144411, India
| |
Collapse
|
12
|
Garcia Ruiz MT, Knapp AN, Garcia-Ruiz H. Profile of genetically modified plants authorized in Mexico. GM CROPS & FOOD 2018; 9:152-168. [PMID: 30388927 PMCID: PMC6277063 DOI: 10.1080/21645698.2018.1507601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 07/11/2018] [Accepted: 07/26/2018] [Indexed: 11/03/2022]
Abstract
Mexico is a center of origin for several economically important plants including maize, cotton, and cocoa. Maize represents more than a food crop, has been declared a biological, cultural, agricultural and economic patrimony, and is linked to the national identity of Mexicans. In this review, we describe the historic and current use of genetically modified plants in Mexico and factors that contributed to the development of the biosafety regulation. We developed a database containing all permit applications received by the government to release genetically modified plants. A temporal and geographical analysis identified the plant species that have been authorized for experimental purposes, pilot programs, or commercial production, the geographic areas where they have been released, and the traits that have been introduced. Results show that Mexico has faced a dual challenge: accepting the benefits of genetically modified plants and their products, while protecting native plant biodiversity.
Collapse
Affiliation(s)
| | - Aaron N. Knapp
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, NE, USA
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, NE, USA
| |
Collapse
|
13
|
Tashkandi M, Ali Z, Aljedaani F, Shami A, Mahfouz MM. Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. PLANT SIGNALING & BEHAVIOR 2018. [PMID: 30289378 DOI: 10.1080/15592324.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
Collapse
Affiliation(s)
- Manal Tashkandi
- a Laboratory for Genome Engineering, Division of Biological Sciences , 4700 King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Zahir Ali
- a Laboratory for Genome Engineering, Division of Biological Sciences , 4700 King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Fatimah Aljedaani
- a Laboratory for Genome Engineering, Division of Biological Sciences , 4700 King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Ashwag Shami
- a Laboratory for Genome Engineering, Division of Biological Sciences , 4700 King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
- b College of Science, Biology Department , Kingdom of Saudi Arabia (KSA), Princess Nourah bint Abdulrahman University , Riyadh , Saudi Arabia
| | - Magdy M Mahfouz
- a Laboratory for Genome Engineering, Division of Biological Sciences , 4700 King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| |
Collapse
|
14
|
Potential impact of genome editing in world agriculture. Emerg Top Life Sci 2017; 1:117-133. [PMID: 33525764 DOI: 10.1042/etls20170010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/22/2017] [Accepted: 09/28/2017] [Indexed: 12/26/2022]
Abstract
Changeable biotic and abiotic stress factors that affect crop growth and productivity, alongside a drive to reduce the unintended consequences of plant protection products, will demand highly adaptive farm management practices as well as access to continually improved seed varieties. The former is limited mainly by cost and, in theory, could be implemented in relatively short time frames. The latter is fundamentally a longer-term activity where genome editing can play a major role. The first targets for genome editing will inevitably be loss-of-function alleles, because these are straightforward to generate. In addition, they are likely to focus on traits under simple genetic control and where the results of modification are already well understood from null alleles in existing gene pools or other knockout or silencing approaches such as induced mutations or RNA interference. In the longer term, genome editing will underpin more fundamental changes in agricultural performance and food quality, and ultimately will merge with the tools and philosophies of synthetic biology to underpin and enable new cellular systems, processes and organisms completely. The genetic changes required for simple allele edits or knockout phenotypes are synonymous with those found naturally in conventional breeding material and should be regulated as such. The more radical possibilities in the longer term will need societal engagement along with appropriate safety and ethical oversight.
Collapse
|
15
|
Opportunities for genome editing in vegetable crops. Emerg Top Life Sci 2017; 1:193-207. [DOI: 10.1042/etls20170033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 11/17/2022]
Abstract
Vegetables include high-value crops with health-promoting effects and reduced environmental impact. The availability of genomic and biotechnological tools in certain species, coupled with the recent development of new breeding techniques based on precise editing of DNA, provides unique opportunities to finally take advantage of the past decades of detailed genetic analyses, thus making improvement of traits related to quality and stress tolerance achievable in a reasonable time frame. Recent reports of such approaches in vegetables illustrate the feasibility of obtaining multiple homozygous mutations in a single generation, heritable by the progeny, using stable or transient transformation approaches, which may not rely on the integration of unwanted foreign DNA. Application of these approaches to currently non-sequenced/tissue culture recalcitrant crops will contribute to meet the challenges posed by the increase in population and climate change.
Collapse
|