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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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Prajapati A, Nain V, Singh D. Designed gRNAs for CRISPR-Cas9 based antifungal resistance in eggplant. Bioinformation 2023; 19:844-848. [PMID: 37908609 PMCID: PMC10613811 DOI: 10.6026/97320630019844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 11/02/2023] Open
Abstract
Eggplant is an important vegetable crop and is a good source of antioxidants, minerals, and vitamins. It has been used in ancient medicines for the treatment of multiple diseases. However, the cultivated varieties of eggplant are susceptible to numerous pathogens and pests that have a negative impact on vegetable crops. Increased resistance achieved through resistance genes (R genes) is limited in eggplant breeding due to the fact that R genes are typically specific to a pathogen race and can be quickly surpassed by pathogen evolution. The susceptibility genes (S genes) in plants facilitate pathogen entry and proliferation, thus disabling these genes might be beneficial for providing a broad range and durable resistance against pathogens. Reports on crops such as Arabidopsis, rice, wheat, citrus, and tomatoes have highlighted that the knockout mutants of the S genes are tolerant to multiple different pathogens. The CRISPR/Cas9 system facilitates plant genome editing that can be utilized efficiently for crop improvement. In the current work, we have identified the homologs of candidate S genes DMR1, DMR6, EDR1, and PMR4/5/6 in the eggplant genome and designed and screened putative gRNAs against the identified target loci. The gRNAs were screened and selected on the basis of recognition of the PAM sequence, the MIT score, their minimum free energy, and the secondary structure. Five gRNAs for each gene homolog were selected after an in-depth analysis of all the predicted gRNAs using the above-mentioned criterion.
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Affiliation(s)
- Archana Prajapati
- />School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India
| | - Vikrant Nain
- />School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India
| | - Deepali Singh
- />School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India
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Laura M, Forti C, Barberini S, Ciorba R, Mascarello C, Giovannini A, Pistelli L, Pieracci Y, Lanteri AP, Ronca A, Minuto A, Ruffoni B, Cardi T, Savona M. Highly Efficient CRISPR/Cas9 Mediated Gene Editing in Ocimum basilicum 'FT Italiko' to Induce Resistance to Peronospora belbahrii. PLANTS (BASEL, SWITZERLAND) 2023; 12:2395. [PMID: 37446956 DOI: 10.3390/plants12132395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Ocimum basilicum (sweet basil) is an economically important aromatic herb; in Italy, approximately 1000 ha of "Genovese-type" basil are grown annually in greenhouses and open fields and are subjected to Downy Mildew (DM) disease, caused by Peronospora belbahrii, leading to huge crop losses. Mutation of the Susceptibility (S) gene DMR6 (Downy Mildew Resistant 6) has been proven to confer a broad-spectrum resistance to DM. In this work, an effective Genome Editing (GE) approach mediated by CRISPR/Cas9 in O. basilicum 'Italiko', the élite cultivar used to produce "Pesto Genovese D.O.P", was developed. A highly efficient genetic transformation method mediated by A. tumefaciens has been optimized from cotyledonary nodes, obtaining 82.2% of regenerated shoots, 84.6% of which resulted in Cas9+ plants. Eleven T0 lines presented different type of mutations in ObDMR6; 60% were indel frameshift mutations with knock-out of ObDMR6 of 'FT Italiko'. Analysis of six T1 transgene-free seedlings revealed that the mutations of T0 plants were inherited and segregated. Based on infection trials conducted on T0 plants, clone 22B showed a very low percentage of disease incidence after 14 days post infection. The aromatic profile of all in vitro edited plants was also reported; all of them showed oxygenated monoterpenes as the major fraction.
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Affiliation(s)
- Marina Laura
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - Chiara Forti
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
- CNR-IBBA, Institute of Agricultural Biology and Biotechnology, Via Bassini 12, 20133 Milano, Italy
| | - Sara Barberini
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
- CNR-IPSP, Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Roberto Ciorba
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
- CREA, Research Centre for Olive, Fruit and Citrus Crops, Via di Fioranello 52, 00134 Rome, Italy
| | - Carlo Mascarello
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - Annalisa Giovannini
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - Luisa Pistelli
- Department of Pharmacy, University of Pisa, Via Bonanno 33, 56126 Pisa, Italy
| | - Ylenia Pieracci
- Department of Pharmacy, University of Pisa, Via Bonanno 33, 56126 Pisa, Italy
| | - Anna Paola Lanteri
- CeRSAA, Center for Agricultural Experimentation and Assistance, Regione Rollo 98, 17031 Albenga, Italy
| | - Agostina Ronca
- CeRSAA, Center for Agricultural Experimentation and Assistance, Regione Rollo 98, 17031 Albenga, Italy
| | - Andrea Minuto
- CeRSAA, Center for Agricultural Experimentation and Assistance, Regione Rollo 98, 17031 Albenga, Italy
| | - Barbara Ruffoni
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - Teodoro Cardi
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
- CNR-IBBR, Institute of Biosciences and Bioresources, 80055 Portici, Italy
| | - Marco Savona
- CREA, Research Centre for Vegetable and Ornamental Crops, Corso degli Inglesi 508, 18038 Sanremo, Italy
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Li R, Maioli A, Lanteri S, Moglia A, Bai Y, Acquadro A. Genomic Analysis Highlights Putative Defective Susceptibility Genes in Tomato Germplasm. PLANTS (BASEL, SWITZERLAND) 2023; 12:2289. [PMID: 37375913 DOI: 10.3390/plants12122289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most widely grown vegetables in the world and is impacted by many diseases which cause yield reduction or even crop failure. Breeding for disease resistance is thus a key objective in tomato improvement. Since disease arises from a compatible interaction between a plant and a pathogen, a mutation which alters a plant susceptibility (S) gene facilitating compatibility may induce broad-spectrum and durable plant resistance. Here, we report on a genome-wide analysis of a set of 360 tomato genotypes, with the goal of identifying defective S-gene alleles as a potential source for the breeding of resistance. A set of 125 gene homologs of 10 S-genes (PMR 4, PMR5, PMR6, MLO, BIK1, DMR1, DMR6, DND1, CPR5, and SR1) were analyzed. Their genomic sequences were examined and SNPs/indels were annotated using the SNPeff pipeline. A total of 54,000 SNPs/indels were identified, among which 1300 were estimated to have a moderate impact (non-synonymous variants), while 120 were estimated to have a high impact (e.g., missense/nonsense/frameshift variants). The latter were then analyzed for their effect on gene functionality. A total of 103 genotypes showed one high-impact mutation in at least one of the scouted genes, while in 10 genotypes, more than 4 high-impact mutations in as many genes were detected. A set of 10 SNPs were validated through Sanger sequencing. Three genotypes carrying high-impact homozygous SNPs in S-genes were infected with Oidium neolycopersici, and two highlighted a significantly reduced susceptibility to the fungus. The existing mutations fall within the scope of a history of safe use and can be useful to guide risk assessment in evaluating the effect of new genomic techniques.
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Affiliation(s)
- Ruiling Li
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Alex Maioli
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Sergio Lanteri
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Andrea Moglia
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Alberto Acquadro
- Plant Genetics and Breeding, Department of Agricultural, Forest and Food Science (DISAFA), University of Torino, 10095 Grugliasco, Italy
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Tör M, Wood T, Webb A, Göl D, McDowell JM. Recent developments in plant-downy mildew interactions. Semin Cell Dev Biol 2023; 148-149:42-50. [PMID: 36670035 DOI: 10.1016/j.semcdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/20/2023]
Abstract
Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.
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Affiliation(s)
- Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
| | | | | | - Deniz Göl
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - John M McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061-0329, USA
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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Assou J, Zhang D, Roth KDR, Steinke S, Hust M, Reinard T, Winkelmann T, Boch J. Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:649-663. [PMID: 34784073 DOI: 10.1111/tpj.15584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 05/21/2023]
Abstract
Food allergies are a major health issue worldwide. Modern breeding techniques such as genome editing via CRISPR/Cas9 have the potential to mitigate this by targeting allergens in plants. This study addressed the major allergen Bra j I, a seed storage protein of the 2S albumin class, in the allotetraploid brown mustard (Brassica juncea). Cotyledon explants of an Indian gene bank accession (CR2664) and the German variety Terratop were transformed using Agrobacterium tumefaciens harboring binary vectors with multiple single guide RNAs to induce either large deletions or frameshift mutations in both Bra j I homoeologs. A total of 49 T0 lines were obtained with up to 3.8% transformation efficiency. Four lines had large deletions of 566 up to 790 bp in the Bra j IB allele. Among 18 Terratop T0 lines, nine carried indels in the targeted regions. From 16 analyzed CR2664 T0 lines, 14 held indels and three had all four Bra j I alleles mutated. The majority of the CRISPR/Cas9-induced mutations were heritable to T1 progenies. In some edited lines, seed formation and viability were reduced and seeds showed a precocious development of the embryo leading to a rupture of the testa already in the siliques. Immunoblotting using newly developed Bra j I-specific antibodies revealed the amount of Bra j I protein to be reduced or absent in seed extracts of selected lines. Removing an allergenic determinant from mustard is an important first step towards the development of safer food crops.
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Affiliation(s)
- Juvenal Assou
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Dingbo Zhang
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Kristian D R Roth
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Reinard
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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Zhang X, Low YC, Lawton MA, Simon JE, Di R. CRISPR-Editing of Sweet Basil ( Ocimum basilicum L.) Homoserine Kinase Gene for Improved Downy Mildew Disease Resistance. Front Genome Ed 2021; 3:629769. [PMID: 34713253 PMCID: PMC8525366 DOI: 10.3389/fgeed.2021.629769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Sweet basil (Ocimum basilicum L.) downy mildew disease (DM) caused by Peronospora belbahrii is a worldwide threat to the basil industry due to the lack of natural genetic resistance in sweet basil germplasm collections. In this study, we used CRISPR-gene editing to modify the sweet basil DM susceptibility gene homoserine kinase (ObHSK). Gene-edited plants challenged with P. belbahrii displayed a significantly reduced susceptibility to DM, based on phenotypic disease indices and on in planta pathogen load. These results suggest that ObHSK plays a role in conditioning DM susceptibility, similar to that observed for the AtHSK gene in Arabidopsis. These results demonstrate the utility of CRISPR-gene editing in enhancing DM resistance and contributing to sweet basil breeding programs.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Yee Chen Low
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Michael A Lawton
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - James E Simon
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Rong Di
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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Paul NC, Park SW, Liu H, Choi S, Ma J, MacCready JS, Chilvers MI, Sang H. Plant and Fungal Genome Editing to Enhance Plant Disease Resistance Using the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2021; 12:700925. [PMID: 34447401 PMCID: PMC8382960 DOI: 10.3389/fpls.2021.700925] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/30/2021] [Indexed: 05/10/2023]
Abstract
Crop production has been substantially reduced by devastating fungal and oomycete pathogens, and these pathogens continue to threaten global food security. Although chemical and cultural controls have been used for crop protection, these involve continuous costs and time and fungicide resistance among plant pathogens has been increasingly reported. The most efficient way to protect crops from plant pathogens is cultivation of disease-resistant cultivars. However, traditional breeding approaches are laborious and time intensive. Recently, the CRISPR/Cas9 system has been utilized to enhance disease resistance among different crops such as rice, cacao, wheat, tomato, and grape. This system allows for precise genome editing of various organisms via RNA-guided DNA endonuclease activity. Beyond genome editing in crops, editing the genomes of fungal and oomycete pathogens can also provide new strategies for plant disease management. This review focuses on the recent studies of plant disease resistance against fungal and oomycete pathogens using the CRISPR/Cas9 system. For long-term plant disease management, the targeting of multiple plant disease resistance mechanisms with CRISPR/Cas9 and insights gained by probing fungal and oomycete genomes with this system will be powerful approaches.
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Affiliation(s)
- Narayan Chandra Paul
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Sung-Won Park
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Haifeng Liu
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Sungyu Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jihyeon Ma
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Joshua S. MacCready
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
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Gurav TP, Dholakia BB, Giri AP. A glance at the chemodiversity of Ocimum species: Trends, implications, and strategies for the quality and yield improvement of essential oil. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2021; 21:879-913. [PMID: 34366748 PMCID: PMC8326315 DOI: 10.1007/s11101-021-09767-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/08/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Ocimum species represent commercially important medicinal and aromatic plants. The essential oil biosynthesized by Ocimum species is enriched with specialized metabolites specifically, terpenoids and phenylpropanoids. Interestingly, various Ocimum species are known to exhibit diverse chemical profiles, and this chemical diversity has been at the center of many studies to identify commercially important chemotypes. Here, we present various chemotypes from the Ocimum species and emphasize trends, implications, and strategies for the quality and yield improvement of essential oil. Globally, many Ocimum species have been analyzed for their essential oil composition in over 50 countries. Asia represents the highest number of chemotypes, followed by Africa, South America, and Europe. Ocimum basilicum L. has been the most widespread and well-studied species, followed by O. gratissimum L., O. tenuiflorum L., O. canum Sims, O. americanum and O. kilimandscharicum Gürke. Moreover, various molecular reasons, benefits, adverse health effects and mechanisms behind this vast chemodiversity have been discussed. Different strategies of plant breeding, metabolic engineering, transgenic, and tissue-culture, along with anatomical modifications, are surveyed to enhance specific chemotypic profiles and essential oil yield in numerous Ocimum species. Consequently, chemical characterization of the essential oil obtained from Ocimum species has become indispensable for its proper utilization. The present chemodiversity knowledge from Ocimum species will help to exploit various applications in the industrial, agriculture, biopharmaceutical, and food sectors. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11101-021-09767-z.
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Affiliation(s)
- Tanuja P. Gurav
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008 India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | | | - Ashok P. Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008 India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
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Hasley JAR, Navet N, Tian M. CRISPR/Cas9-mediated mutagenesis of sweet basil candidate susceptibility gene ObDMR6 enhances downy mildew resistance. PLoS One 2021; 16:e0253245. [PMID: 34111225 PMCID: PMC8191900 DOI: 10.1371/journal.pone.0253245] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/31/2021] [Indexed: 11/27/2022] Open
Abstract
Sweet basil (Ocimum basilicum) is an economically important allotetraploid (2n = 4x = 48) herb whose global production is threatened by downy mildew disease caused by the obligate biotrophic oomycete, Peronospora belbahrii. Generation of disease resistant cultivars by mutagenesis of susceptibility (S) genes via CRISPR/Cas9 is currently one of the most promising strategies to maintain favored traits while improving disease resistance. Previous studies have identified Arabidopsis DMR6 (Downy Mildew Resistance 6) as an S gene required for pathogenesis of the downy mildew-causing oomycete pathogen Hyaloperonospora arabidopsidis. In this study, a sweet basil homolog of DMR6, designated ObDMR6, was identified in the popular sweet basil cultivar Genoveser and found to exist with a high copy number in the genome with polymorphisms among the variants. Two CRISPR/Cas9 constructs expressing one or two single guide RNAs (sgRNAs) targeting the conserved regions of ObDMR6 variants were generated and used to transform Genoveser via Agrobacterium-mediated transformation. 56 T0 lines were generated, and mutations of ObDMR6 were detected by analyzing the Sanger sequencing chromatograms of an ObDMR6 fragment using the Interference of CRISPR Edits (ICE) software. Among 54 lines containing mutations in the targeted sites, 13 had an indel percentage greater than 96% suggesting a near-complete knockout (KO) of ObDMR6. Three representative transgene-free lines with near-complete KO of ObDMR6 determined by ICE were identified in the T1 segregating populations derived from three independent T0 lines. The mutations were further confirmed using amplicon deep sequencing. Disease assays conducted on T2 seedlings of the above T1 lines showed a reduction in production of sporangia by 61-68% compared to the wild-type plants and 69-93% reduction in relative pathogen biomass determined by quantitative PCR (qPCR). This study not only has generated transgene-free sweet basil varieties with improved downy mildew resistance, but also contributed to our understanding of the molecular interactions of sweet basil-P. belbahrii.
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Affiliation(s)
- Jeremieh Abram R. Hasley
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Natasha Navet
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Miaoying Tian
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
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Li C, Brant E, Budak H, Zhang B. CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 2021; 22:253-284. [PMID: 33835761 PMCID: PMC8042526 DOI: 10.1631/jzus.b2100009] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.
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Affiliation(s)
- Chao Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Eleanor Brant
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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Gonda I, Faigenboim A, Adler C, Milavski R, Karp MJ, Shachter A, Ronen G, Baruch K, Chaimovitsh D, Dudai N. The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding. DNA Res 2020; 27:6042144. [PMID: 33340318 PMCID: PMC7758295 DOI: 10.1093/dnares/dsaa027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers.
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Affiliation(s)
- Itay Gonda
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Adi Faigenboim
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Chen Adler
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Renana Milavski
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Merrie-Jean Karp
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Alona Shachter
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | | | - David Chaimovitsh
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Nativ Dudai
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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15
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Navet N, Tian M. Agrobacterium-mediated Transformation of Sweet Basil ( Ocimum basilicum). Bio Protoc 2020; 10:e3828. [PMID: 33659480 DOI: 10.21769/bioprotoc.3828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/02/2022] Open
Abstract
Sweet basil (Ocimum basilicum) is a popular herb with high economic value and is currently threatened by a severe oomycete disease. An efficient transformation method is a prerequisite for gene functional analysis to accelerate molecular breeding and deploy effective disease management strategies, and breeding through genetic engineering. Here we present a detailed protocol for a highly efficient Agrobacterium tumefaciens-mediated transformation method for sweet basil, which was established based on a previously reported method by other researchers, with modifications on several aspects, including growth of sweet basil, age of plants used for explants, preparation and concentration of Agrobacteria. This protocol allows researchers in academia and agroindustry to generate transgenic sweet basil plants in an easy, quick and highly reproducible manner. In addition, this protocol may be applicable to transform other species within the genus Ocimum.
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Affiliation(s)
- Natasha Navet
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, USA
| | - Miaoying Tian
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, USA
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