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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024:PHYTO03240084RVW. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Jia H, Omar AA, Xu J, Dalmendray J, Wang Y, Feng Y, Wang W, Hu Z, Grosser JW, Wang N. Generation of transgene-free canker-resistant Citrus sinensis cv. Hamlin in the T0 generation through Cas12a/CBE co-editing. FRONTIERS IN PLANT SCIENCE 2024; 15:1385768. [PMID: 38595767 PMCID: PMC11002166 DOI: 10.3389/fpls.2024.1385768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Citrus canker disease affects citrus production. This disease is caused by Xanthomonas citri subsp. citri (Xcc). Previous studies confirmed that during Xcc infection, PthA4, a transcriptional activator like effector (TALE), is translocated from the pathogen to host plant cells. PthA4 binds to the effector binding elements (EBEs) in the promoter region of canker susceptibility gene LOB1 (EBEPthA4-LOBP) to activate its expression and subsequently cause canker symptoms. Previously, the Cas12a/CBE co-editing method was employed to disrupt EBEPthA4-LOBP of pummelo, which is highly homozygous. However, most commercial citrus cultivars are heterozygous hybrids and more difficult to generate homozygous/biallelic mutants. Here, we employed Cas12a/CBE co-editing method to edit EBEPthA4-LOBP of Hamlin (Citrus sinensis), a commercial heterozygous hybrid citrus cultivar grown worldwide. Binary vector GFP-p1380N-ttLbCas12a:LOBP1-mPBE:ALS2:ALS1 was constructed and shown to be functional via Xcc-facilitated agroinfiltration in Hamlin leaves. This construct allows the selection of transgene-free regenerants via GFP, edits ALS to generate chlorsulfuron-resistant regenerants as a selection marker for genome editing resulting from transient expression of the T-DNA via nCas9-mPBE:ALS2:ALS1, and edits gene(s) of interest (i.e., EBEPthA4-LOBP in this study) through ttLbCas12a, thus creating transgene-free citrus. Totally, 77 plantlets were produced. Among them, 8 plantlets were transgenic plants (#HamGFP1 - #HamGFP8), 4 plantlets were transgene-free (#HamNoGFP1 - #HamNoGFP4), and the rest were wild type. Among 4 transgene-free plantlets, three lines (#HamNoGFP1, #HamNoGFP2 and #HamNoGFP3) contained biallelic mutations in EBEpthA4, and one line (#HamNoGFP4) had homozygous mutations in EBEpthA4. We achieved 5.2% transgene-free homozygous/biallelic mutation efficiency for EBEPthA4-LOBP in C. sinensis cv. Hamlin, compared to 1.9% mutation efficiency for pummelo in a previous study. Importantly, the four transgene-free plantlets and 3 transgenic plantlets that survived were resistant against citrus canker. Taken together, Cas12a/CBE co-editing method has been successfully used to generate transgene-free canker-resistant C. sinensis cv. Hamlin in the T0 generation via biallelic/homozygous editing of EBEpthA4 of the canker susceptibility gene LOB1.
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Affiliation(s)
- Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Ahmad A. Omar
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Javier Dalmendray
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Yu Feng
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Wenting Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Zhuyuan Hu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
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Campa M, Miranda S, Licciardello C, Lashbrooke JG, Dalla Costa L, Guan Q, Spök A, Malnoy M. Application of new breeding techniques in fruit trees. PLANT PHYSIOLOGY 2024; 194:1304-1322. [PMID: 37394947 DOI: 10.1093/plphys/kiad374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
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Affiliation(s)
- Manuela Campa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Simón Miranda
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | | | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Mickael Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
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Gill RA, Li X, Duan S, Xing Q, Müller-Xing R. Citrus threat huanglongbing (HLB) - Could the rootstock provide the cure? FRONTIERS IN PLANT SCIENCE 2024; 15:1330846. [PMID: 38405591 PMCID: PMC10885694 DOI: 10.3389/fpls.2024.1330846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Affiliation(s)
- Rafaqat A. Gill
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- College of Life Science, Nanchang University, Nanchang, China
| | - Xianglian Li
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- College of Life Science, Nanchang University, Nanchang, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Qian Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- College of Life Science, Nanchang University, Nanchang, China
| | - Ralf Müller-Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- College of Life Science, Nanchang University, Nanchang, China
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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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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Xu J, Zhang Y, Li J, Teper D, Sun X, Jones D, Wang Y, Tao J, Goss EM, Jones JB, Wang N. Phylogenomic analysis of 343 Xanthomonas citri pv. citri strains unravels introduction history and dispersal paths. PLoS Pathog 2023; 19:e1011876. [PMID: 38100539 PMCID: PMC10756548 DOI: 10.1371/journal.ppat.1011876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Xanthomonas citri pv. citri (Xcc) causes the devastating citrus canker disease. Xcc is known to have been introduced into Florida, USA in at least three different events in 1915, 1986 and 1995 with the first two claimed to be eradicated. It was questioned whether the Xcc introduction in 1986 has been successfully eradicated. Furthermore, it is unknown how Xcc has spread throughout the citrus groves in Florida. In this study, we investigated the population structure of Xcc to address these questions. We sequenced the whole genome of 343 Xcc strains collected from Florida groves between 1997 and 2016. Our analysis revealed two distinct clusters of Xcc. Our data strongly indicate that the claimed eradication of the 1986 Xcc introduction was not successful and Xcc strains from 1986 introduction were present in samples from at least 8 counties collected after 1994. Importantly, our data revealed that the Cluster 2 strains, which are present in all 20 citrus-producing counties sampled in Florida, originated from the Xcc introduction event in the Miami area in 1995. Our data suggest that Polk County is the epicenter of the dispersal of Cluster 2 Xcc strains, which is consistent with the fact that three major hurricanes passed through Polk County in 2004. As copper-based products have been extensively used to control citrus canker, we also investigated whether Xcc strains have developed resistance to copper. Notably, none of the 343 strains contained known copper resistance genes. Twenty randomly selected Xcc strains displayed sensitivity to copper. Overall, this study provides valuable insights into the introduction, eradication, spread, and copper resistance of Xcc in Florida.
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Affiliation(s)
- Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Yanan Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Xiaoan Sun
- Florida Department of Agriculture and Consumer Services, Gainesville, Florida, United States of America
| | - Debra Jones
- Florida Department of Agriculture and Consumer Services, Gainesville, Florida, United States of America
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jin Tao
- Guangdong Magigene Biotechnology Co., Ltd., Guangzhou, China
| | - Erica M. Goss
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jeffrey B. Jones
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
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Gao L, Kumaravel K, Xiong Q, Liang Y, Ju Z, Jiang Y, Zhang J. Actinomycins produced by endophyte Streptomyces sp. GLL-9 from navel orange plant exhibit high antimicrobial effect against Xanthomonas citri susp. citri and Penicillium italicum. PEST MANAGEMENT SCIENCE 2023; 79:4679-4693. [PMID: 37450767 DOI: 10.1002/ps.7668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/21/2023] [Accepted: 07/15/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Citrus canker and citrus blue mold are two severe diseases in citrus plants, which are mainly caused by Xanthomonas citri susp. citri (Xcc) and Penicillium italicum, respectively. The currently widely used pesticides for these two diseases are harmful to human health and the environment. Therefore, searching for novel antimicrobial agents, especially from natural resources, is getting increasing interest. RESULTS In this study, the crude extract of Streptomyces sp. GLL-9, an endophyte from a navel orange tree, was found to exhibit excellent antimicrobial effects against Xcc and P. italicum. Bioassay-guided isolation led to the discovery of three actinomycins (Acts), actinomycin X2 (Act-X2 ), actinomycin D (ActD), and actinomycin XOβ (Act-XOβ ). The MIC (minimum inhibitory concentration) values of Act-X2 , ActD, and Act-XOβ were 31.25, 62.50, and 62.50 μg mL-1 against Xcc, respectively, while 62.50 (Act-X2 ) and 125.00 μg mL-1 (ActD) against P. italicum, being better or comparable to the positive controls. The highest yield of Acts was obtained by solid-state fermentation with rice containing 1% L-tryptophan as a culture medium, being 6.03, 3.07, and 1.02 mg g-1 , for Act-X2 , ActD, and Act-XOβ , respectively. The ethyl acetate extract of Streptomyces sp. GLL-9 cultivated under the optimal fermentation conditions (EAE-1) can efficiently control these two citrus diseases by excessively producing reactive oxygen species (ROS) in both pathogens, damaging the cell membranes of P. italicum, and inhibiting the growth of Xcc. In addition, Act-X2 , ActD, and EAE-1 displayed broad-spectrum antifungal activity. CONCLUSION EAE-1 and Acts produced by Streptomyces sp. GLL-9 have high potential as novel antimicrobial agents against plant pathogens. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Liangliang Gao
- National Engineering Research Center of Navel Orange, Gannan Normal University, Ganzhou, China
| | - Kaliaperumal Kumaravel
- Department of Orthodontics, Saveetha Dental College, Saveetha University, Chennai, India
| | - Qin Xiong
- National Engineering Research Center of Navel Orange, Gannan Normal University, Ganzhou, China
| | - Yan Liang
- National Engineering Research Center of Navel Orange, Gannan Normal University, Ganzhou, China
| | - Zhiran Ju
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
| | - Yueming Jiang
- National Engineering Research Center of Navel Orange, Gannan Normal University, Ganzhou, China
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
| | - Jun Zhang
- National Engineering Research Center of Navel Orange, Gannan Normal University, Ganzhou, China
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
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Shantharaj D, Minsavage GV, Orbović V, Moore GA, Holmes DR, Römer P, Horvath DM, Lahaye T, Jones JB. A promoter trap in transgenic citrus mediates recognition of a broad spectrum of Xanthomonas citri pv. citri TALEs, including in planta-evolved derivatives. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2019-2032. [PMID: 37421233 PMCID: PMC10502743 DOI: 10.1111/pbi.14109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/10/2023]
Abstract
Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri (Xcc), causes dramatic losses to the citrus industry worldwide. Transcription activator-like effectors (TALEs), which bind to effector binding elements (EBEs) in host promoters and activate transcription of downstream host genes, contribute significantly to Xcc virulence. The discovery of the biochemical context for the binding of TALEs to matching EBE motifs, an interaction commonly referred to as the TALE code, enabled the in silico prediction of EBEs for each TALE protein. Using the TALE code, we engineered a synthetic resistance (R) gene, called the Xcc-TALE-trap, in which 14 tandemly arranged EBEs, each capable of autonomously recognizing a particular Xcc TALE, drive the expression of Xanthomonas avrGf2, which encodes a bacterial effector that induces plant cell death. Analysis of a corresponding transgenic Duncan grapefruit showed that transcription of the cell death-inducing executor gene, avrGf2, was strictly TALE-dependent and could be activated by several different Xcc TALE proteins. Evaluation of Xcc strains from different continents showed that the Xcc-TALE-trap mediates resistance to this global panel of Xcc isolates. We also studied in planta-evolved TALEs (eTALEs) with novel DNA-binding domains and found that these eTALEs also activate the Xcc-TALE-trap, suggesting that the Xcc-TALE-trap is likely to confer durable resistance to Xcc. Finally, we show that the Xcc-TALE-trap confers resistance not only in laboratory infection assays but also in more agriculturally relevant field studies. In conclusion, transgenic plants containing the Xcc-TALE-trap offer a promising sustainable approach to control CBC.
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Affiliation(s)
| | | | - Vladimir Orbović
- Citrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
| | - Gloria A. Moore
- Department of Horticultural SciencesUniversity of FloridaGainesvilleFLUSA
| | - Danalyn R. Holmes
- Zentrum für Molekularbiologie der Pflanzen (ZMBP)Eberhard‐Karls‐Universität TübingenTübingenGermany
| | - Patrick Römer
- Genetics, Department of BiologyLudwig‐Maximilians‐University MunichMartinsriedGermany
- Present address:
Avicare+KöthenGermany
| | | | - Thomas Lahaye
- Zentrum für Molekularbiologie der Pflanzen (ZMBP)Eberhard‐Karls‐Universität TübingenTübingenGermany
- Genetics, Department of BiologyLudwig‐Maximilians‐University MunichMartinsriedGermany
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10
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Huang X, Jia H, Xu J, Wang Y, Wen J, Wang N. Transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation via a co-editing strategy. NATURE PLANTS 2023; 9:1591-1597. [PMID: 37723203 DOI: 10.1038/s41477-023-01520-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Transgene-free plant genome editing in the T0 generation is highly desirable but challenging1,2. Here we achieved such a goal using a co-editing strategy via Agrobacterium-mediated transient expression of cytosine base editor to edit ALS encoding acetolactate synthase to confer herbicide chlorsulfuron resistance as a selection marker, Cas12a/CRISPR RNA for editing gene(s) of interest, and green fluorescent protein for selecting transgene-free transformants. The biallelic/homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 1.9% to 42.1% in tomato, tobacco, potato and citrus. This co-editing strategy is particularly useful for transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation.
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Affiliation(s)
- Xiaoen Huang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jiawen Wen
- Citrus Research and Education Center, Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
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11
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Sardar A. Genetic amelioration of fruit and vegetable crops to increase biotic and abiotic stress resistance through CRISPR Genome Editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1260102. [PMID: 37841604 PMCID: PMC10570431 DOI: 10.3389/fpls.2023.1260102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Environmental changes and increasing population are major concerns for crop production and food security as a whole. To address this, researchers had focussed on the improvement of cereals and pulses and have made considerable progress till the beginning of this decade. However, cereals and pulses together, without vegetables and fruits, are inadequate to meet the dietary and nutritional demands of human life. Production of good quality vegetables and fruits is highly challenging owing to their perishable nature and short shelf life as well as abiotic and biotic stresses encountered during pre- and post-harvest. Genetic engineering approaches to produce good quality, to increase shelf life and stress-resistance, and to change the time of flowering and fruit ripening by introducing foreign genes to produce genetically modified crops were quite successful. However, several biosafety concerns, such as the risk of transgene-outcrossing, limited their production, marketing, and consumption. Modern genome editing techniques, like the CRISPR/Cas9 system, provide a perfect solution in this scenario, as it can produce transgene-free genetically edited plants. Hence, these genetically edited plants can easily satisfy the biosafety norms for crop production and consumption. This review highlights the potential of the CRISPR/Cas9 system for the successful generation of abiotic and biotic stress resistance and thereby improving the quality, yield, and overall productivity of vegetables and fruits.
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Affiliation(s)
- Atish Sardar
- Department of Botany, Jogesh Chandra Chaudhuri College, West Bengal, Kolkata, India
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12
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Su H, Wang Y, Xu J, Omar AA, Grosser JW, Calovic M, Zhang L, Feng Y, Vakulskas CA, Wang N. Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation. Nat Commun 2023; 14:3957. [PMID: 37402755 DOI: 10.1038/s41467-023-39714-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is a destructive citrus disease worldwide. Generating disease-resistant cultivars is the most effective, environmentally friendly and economic approach for disease control. However, citrus traditional breeding is lengthy and laborious. Here, we develop transgene-free canker-resistant Citrus sinensis lines in the T0 generation within 10 months through transformation of embryogenic protoplasts with Cas12a/crRNA ribonucleoprotein to edit the canker susceptibility gene CsLOB1. Among the 39 regenerated lines, 38 are biallelic/homozygous mutants, demonstrating a 97.4% biallelic/homozygous mutation rate. No off-target mutations are detected in the edited lines. Canker resistance of the cslob1-edited lines results from both abolishing canker symptoms and inhibiting Xcc growth. The transgene-free canker-resistant C. sinensis lines have received regulatory approval by USDA APHIS and are exempted from EPA regulation. This study provides a sustainable and efficient citrus canker control solution and presents an efficient transgene-free genome-editing strategy for citrus and other crops.
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Affiliation(s)
- Hang Su
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Ahmad A Omar
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jude W Grosser
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Milica Calovic
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Liyang Zhang
- Integrated DNA Technologies, Inc, Coralville, IA, USA
| | - Yu Feng
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | | | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
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13
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de Souza-Neto RR, Vasconcelos FNDC, Teper D, Carvalho IGB, Takita MA, Benedetti CE, Wang N, de Souza AA. The Expansin Gene CsLIEXP1 Is a Direct Target of CsLOB1 in Citrus. PHYTOPATHOLOGY 2023; 113:1266-1277. [PMID: 36825333 DOI: 10.1094/phyto-11-22-0424-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transcription activator-like effectors are key virulence factors of Xanthomonas. They are secreted into host plant cells and mimic transcription factors inducing the expression of host susceptibility (S) genes. In citrus, CsLOB1 is a direct target of PthA4, the primary effector associated with citrus canker symptoms. CsLOB1 is a transcription factor, and its expression is required for canker symptoms induced by Xanthomonas citri subsp. citri. Several genes are up-regulated by PthA4; however, only CsLOB1 was described as an S gene induced by PthA4. Here, we investigated whether other up-regulated genes could be direct targets of PthA4 or CsLOB1. Seven up-regulated genes by PthA4 were investigated; however, an expansin-coding gene was more induced than CsLOB1. In Nicotiana benthamiana transient expression experiments, we demonstrate that the expansin-coding gene, referred here to as CsLOB1-INDUCED EXPANSIN 1 (CsLIEXP1), is not a direct target of PthA4, but CsLOB1. Interestingly, CsLIEXP1 was induced by CsLOB1 even without the predicted CsLOB1 binding site, which suggested that CsLOB1 has other unknown binding sites. We also investigated the minimum promoter regulated by CsLOB1, and this region and LOB1 domain were conserved among citrus species and relatives, which suggests that the interaction PthA4-CsLOB1-CsLIEXP1 is conserved in citrus species and relatives. This is the first study that experimentally demonstrated a CsLOB1 downstream target and lays the foundation to identify other new targets. In addition, we demonstrated that the CsLIEXP1 is a putative S gene indirectly induced by PthA4, which may serve as the target for genome editing to generate citrus canker-resistant varieties.
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Affiliation(s)
- Reinaldo Rodrigues de Souza-Neto
- Citrus Research Center "Sylvio Moreira", Agronomic Institute-IAC, Brazil
- Departament of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Brazil
| | | | - Doron Teper
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, Volcani Center, Israel
| | | | | | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, U.S.A
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14
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Pandey SS, Xu J, Achor DS, Li J, Wang N. Microscopic and Transcriptomic Analyses of Early Events Triggered by ' Candidatus Liberibacter asiaticus' in Young Flushes of Huanglongbing-Positive Citrus Trees. PHYTOPATHOLOGY 2023; 113:985-997. [PMID: 36449527 DOI: 10.1094/phyto-10-22-0360-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
'Candidatus Liberibacter asiaticus' (CLas) is associated with the devastating citrus disease Huanglongbing (HLB). Young flushes are the center of the HLB pathosystem due to their roles in the psyllid life cycle and in the acquisition and transmission of CLas. However, the early events of CLas infection and how CLas modulates young flush physiology remain poorly understood. Here, transmission electron microscopy analysis showed that the mean diameter of the sieve pores decreased in young leaves of HLB-positive trees after CLas infection, consistent with CLas-triggered callose deposition. RNA-seq-based global expression analysis of young leaves of HLB-positive sweet orange with (CLas-Pos) and without (CLas-Neg) detectable CLas demonstrated a significant impact on gene expression in young leaves, including on the expression of genes involved in host immunity, stress response, and plant hormone biosynthesis and signaling. CLas-Pos and CLas-Neg expression data displayed distinct patterns. The number of upregulated genes was higher than that of the downregulated genes in CLas-Pos for plant-pathogen interactions, glutathione metabolism, peroxisome, and calcium signaling, which are commonly associated with pathogen infections, compared with the healthy control. On the contrary, the number of upregulated genes was lower than that of the downregulated genes in CLas-Neg for genes involved in plant-pathogen interactions and peroxisome biogenesis/metabolism. Additionally, a time-course quantitative reverse transcription-PCR-based expression analysis visualized the induced expression of companion cell-specific genes, phloem protein 2 genes, and sucrose transport genes in young flushes triggered by CLas. This study advances our understanding of early events during CLas infection of citrus young flushes.
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Affiliation(s)
- Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Diann S Achor
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
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15
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Teper D, White FF, Wang N. The Dynamic Transcription Activator-Like Effector Family of Xanthomonas. PHYTOPATHOLOGY 2023; 113:651-666. [PMID: 36449529 DOI: 10.1094/phyto-10-22-0365-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins that are injected into the eukaryotic nucleus to act as transcriptional factors and function as key virulence factors of the phytopathogen Xanthomonas. TALEs are translocated into plant host cells via the type III secretion system and induce the expression of host susceptibility (S) genes to facilitate disease. The unique modular DNA binding domains of TALEs comprise an array of nearly identical direct repeats that enable binding to DNA targets based on the recognition of a single nucleotide target per repeat. The very nature of TALE structure and function permits the proliferation of TALE genes and evolutionary adaptations in the host to counter TALE function, making the TALE-host interaction the most dynamic story in effector biology. The TALE genes appear to be a relatively young effector gene family, with a presence in all virulent members of some species and absent in others. Genome sequencing has revealed many TALE genes throughout the xanthomonads, and relatively few have been associated with a cognate S gene. Several species, including Xanthomonas oryzae pv. oryzae and X. citri pv. citri, have near absolute requirement for TALE gene function, while the genes appear to be just now entering the disease interactions with new fitness contributions to the pathogens of tomato and pepper among others. Deciphering the simple and effective DNA binding mechanism also has led to the development of DNA manipulation tools in fields of gene editing and transgenic research. In the three decades since their discovery, TALE research remains at the forefront of the study of bacterial evolution, plant-pathogen interactions, and synthetic biology. We also discuss critical questions that remain to be addressed regarding TALEs.
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Affiliation(s)
- Doron Teper
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Frank F White
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, U.S.A
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16
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Gao Y, Xu J, Li Z, Zhang Y, Riera N, Xiong Z, Ouyang Z, Liu X, Lu Z, Seymour D, Zhong B, Wang N. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 2023; 26:106024. [PMID: 36824272 PMCID: PMC9941208 DOI: 10.1016/j.isci.2023.106024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.
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Affiliation(s)
- Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhilong Li
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nadia Riera
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhigang Ouyang
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xinjun Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhanjun Lu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | | | - Balian Zhong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
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17
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Ribeiro C, Xu J, Hendrich C, Pandey SS, Yu Q, Gmitter FG, Wang N. Seasonal Transcriptome Profiling of Susceptible and Tolerant Citrus Cultivars to Citrus Huanglongbing. PHYTOPATHOLOGY 2023; 113:286-298. [PMID: 36001783 DOI: 10.1094/phyto-05-22-0179-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Citrus huanglongbing (HLB) caused by 'Candidatus Liberibacter asiaticus' (CLas) is the most devastating citrus disease worldwide. Most commercial citrus cultivars are susceptible to HLB, with a few more tolerant exceptions such as 'LB8-9' Sugar Belle mandarin. Transcriptomic analyses have been widely used to investigate the potential mechanisms for disease susceptibility, resistance, or tolerance. Previous transcriptomic studies related to HLB mostly focused on single time point data collection. We hypothesize that changes in day length and temperature throughout the seasons have profound effects on citrus-CLas interactions. Here, we conducted RNA-seq analyses on HLB-susceptible Valencia sweet orange and HLB-tolerant mandarin 'LB8-9' in winter, spring, summer, and fall. Significant variations in differentially expressed genes (DEGs) related to HLB were observed among the four seasons. For both cultivars, the highest number of DEGs were found in the spring. CLas infection stimulates the expression of immune-related genes such as NBS-LRR, RLK, RLCK, CDPK, MAPK pathway, reactive oxygen species (ROS), and PR genes in both cultivars, consistent with the model that HLB is a pathogen-triggered immune disease. HLB-positive mandarin 'LB8-9' trees contained higher concentrations of maltose and sucrose, which are known to scavenge ROS. In addition, mandarin 'LB8-9' showed higher expression of genes involved in phloem regeneration, which might contribute to its HLB tolerance. This study shed light on the pathogenicity mechanism of the HLB pathosystem and the tolerance mechanism against HLB, providing valuable insights into HLB management.
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Affiliation(s)
- Camila Ribeiro
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Connor Hendrich
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Sheo Shankar Pandey
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Qibin Yu
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Frederick G Gmitter
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
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18
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Saeed S, Usman B, Shim SH, Khan SU, Nizamuddin S, Saeed S, Shoaib Y, Jeon JS, Jung KH. CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111435. [PMID: 36031021 DOI: 10.1016/j.plantsci.2022.111435] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.
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Affiliation(s)
- Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Babar Usman
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University KPK, Pakistan
| | - Sabzoi Nizamuddin
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Sundus Saeed
- School of Engineering, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Yasira Shoaib
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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19
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Ma H, Meng X, Xu K, Li M, Gmitter FG, Liu N, Gai Y, Huang S, Wang M, Wang M, Wang N, Xu H, Liu J, Sun X, Duan S. Highly efficient hairy root genetic transformation and applications in citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:1039094. [PMID: 36388468 PMCID: PMC9647159 DOI: 10.3389/fpls.2022.1039094] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Highly efficient genetic transformation technology is greatly beneficial for crop gene function analysis and precision breeding. However, the most commonly used genetic transformation technology for woody plants, mediated by Agrobacterium tumefaciens, is time-consuming and inefficient, which limits its utility for gene function analysis. In this study, a simple, universal, and highly efficient genetic transformation technology mediated by A. rhizogenes K599 is described. This technology can be applied to multiple citrus genotypes, and only 2-8 weeks were required for the entire workflow. Genome-editing experiments were simultaneously conducted using 11 plasmids targeting different genomic positions and all corresponding transformants with the target knocked out were obtained, indicating that A. rhizogenes-mediated genome editing was highly efficient. In addition, the technology is advantageous for investigation of specific genes (such as ACD2) for obtaining "hard-to-get" transgenic root tissue. Furthermore, A. rhizogenes can be used for direct viral vector inoculation on citrus bypassing the requirement for virion enrichment in tobacco, which facilitates virus-induced gene silencing and virus-mediated gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus that can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by reducing the cost, required workload, experimental period, and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Xinyue Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Fred G. Gmitter
- Citrus Research and Education Center, Horticultural Sciences Department, University of Florida, Lake Alfred, FL, United States
| | - Ningge Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Min Wang
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Horticultural Sciences Department, University of Florida, Lake Alfred, FL, United States
| | - Hairen Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co., LTD, Hangzhou, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida’s Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
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20
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Gouthu S, Mandelli C, Eubanks BA, Deluc LG. Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations. FRONTIERS IN PLANT SCIENCE 2022; 13:979742. [PMID: 36325537 PMCID: PMC9621297 DOI: 10.3389/fpls.2022.979742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.
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Affiliation(s)
- Satyanarayana Gouthu
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Christian Mandelli
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
| | - Britt A. Eubanks
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Laurent G. Deluc
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
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21
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Cardoso JLS, Souza AA, Vieira MLC. Molecular basis for host responses to Xanthomonas infection. PLANTA 2022; 256:84. [PMID: 36114308 DOI: 10.1007/s00425-022-03994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
This review highlights the most relevant and recent updated information available on the defense responses of selected hosts against Xanthomonas spp. Xanthomonas is one of the most important genera of Gram-negative phytopathogenic bacteria, severely affecting the productivity of economically important crops worldwide, colonizing either the vascular system or the mesophyll tissue of the host. Due to its rapid propagation, Xanthomonas poses an enormous challenge to farmers, because it is usually controlled using huge quantities of copper-based chemicals, adversely impacting the environment. Thus, developing new ways of preventing colonization by these bacteria has become essential. Advances in genomic and transcriptomic technologies have significantly elucidated at molecular level interactions between various crops and Xanthomonas species. Understanding how these hosts respond to the infection is crucial if we are to exploit potential approaches for improving crop breeding and cutting productivity losses. This review focuses on our current knowledge of the defense response mechanisms in agricultural crops after Xanthomonas infection. We describe the molecular basis of host-bacterium interactions over a broad spectrum with the aim of improving our fundamental understanding of which genes are involved and how they work in this interaction, providing information that can help to speed up plant breeding programs, namely using gene editing approaches.
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Affiliation(s)
- Jéssica L S Cardoso
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Alessandra A Souza
- Citrus Research Center "Sylvio Moreira", Agronomic Institute (IAC), Cordeirópolis, SP, 13490-000, Brazil
| | - Maria Lucia C Vieira
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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22
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Wang W, Feng M, Li X, Chen F, Zhang Z, Yang W, Shao C, Tao L, Zhang Y. Antibacterial Activity of Aureonuclemycin Produced by Streptomyces aureus Strain SPRI-371. Molecules 2022; 27:molecules27155041. [PMID: 35956994 PMCID: PMC9370760 DOI: 10.3390/molecules27155041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Actinomycetes play a vital role as one of the most important natural resources for both pharmaceutical and agricultural applications. The actinomycete strain SPRI-371, isolated from soil collected in Jiangsu province, China, was classified as Streptomyces aureus based on its morphological, physiological, biochemical and molecular biological characteristics. Its bacterial activity metabolites were identified as aureonuclemycin (ANM), belonging to adenosine derivatives with the molecular formula C16H19N5O9 for ANM A and C10H13N5O3 for ANM B. Simultaneously, the industrial fermentation process of a mutated S. aureus strain SPRI-371 was optimized in a 20 m3 fermentation tank, featuring a rotation speed of 170 rpm, a pressure of 0.05 MPa, an inoculum age of 36−40 h and a dissolved oxygen level maintained at 1−30% within 40−80 h and at >60% in the later period, resulting in an ANM yield of >3700 mg/L. In the industrial separation of fermentation broth, the sulfuric acid solution was selected to adjust pH and 4# resin was used for adsorption. Then, it was resolved with 20% ethanol solution and concentrated in a vacuum (60−65 °C), with excellent results. Antibacterial experiments showed that ANM was less active or inactive against Xanthomonas oryzae pv. oryzae, Xanthomonas citri subsp. citri and Xanthomonas oryzae pv. oryzicola and most bacteria, yeast and fungi in vitro. However, in vivo experiments showed that ANM exhibited extremely significant protective and therapeutic activity against diseases caused by X. oryzae pv. oryzae and X. oryzae pv. oryzicola in rice and X. citri in oranges and lemons. In field trials, ANM A 150 gai/ha + ANM B 75 gai/ha exhibited excellent therapeutic activity against rice bacterial leaf blight, citrus canker and rice bacterial leaf streak. Furthermore, as the dosage and production cost of ANM are lower than those of commercial drugs, it has good application prospects.
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Affiliation(s)
- Weiguo Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Minkang Feng
- Shanghai Jiading District Agricultural Machinery Technology Promotion Station, Shanghai 201800, China
| | - Xiaomeng Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Feiyu Chen
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhihao Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenlong Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chen Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liming Tao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Correspondence:
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23
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Jia H, Wang Y, Su H, Huang X, Wang N. LbCas12a-D156R Efficiently Edits LOB1 Effector Binding Elements to Generate Canker-Resistant Citrus Plants. Cells 2022; 11:cells11030315. [PMID: 35159125 PMCID: PMC8834406 DOI: 10.3390/cells11030315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is an economically important disease in most citrus production regions worldwide. Xcc secretes a transcriptional activator like effector (TALE) PthA4 to bind to the effector binding elements (EBEs) in the promoter region of canker susceptibility gene LOB1 to activate its expression, which in turn causes canker symptoms. Editing the EBE region with Cas9/gRNA has been used to generate canker resistant citrus plants. However, most of the EBE-edited lines generated contain indels of 1–2 bp, which has higher possibility to be overcome by PthA4 adaptation. The adaptation capacity of TALEs inversely correlates with the number of mismatches with the EBE. LbCas12a/crRNA is known to generate longer deletion than Cas9. In this study, we used a temperature-tolerant and more efficient LbCas12a variant (ttLbCas12a), harboring the single substitution D156R, to modify the EBE region of LOB1. We first constructed GFP-p1380N-ttLbCas12a:LOBP, which was shown to be functional via Xcc-facilitated agroinfiltration in Pummelo (Citrus maxima) leaves. Subsequently, we stably expressed ttLbCas12a:LOBP in Pummelo. Eight transgenic lines were generated, with seven lines showing 100% mutations of the EBE, among which one line is homozygous. The EBE-edited lines had the ttLbCas12a-mediated deletions of up to 10 bp. Importantly, the seven lines were canker resistant and no off-targets were detected. In summary, ttLbCas12a can be used to efficiently generate biallelic/homozygous citrus mutant lines with short deletions, thus providing a useful tool for the functional study and breeding of citrus.
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Huang X, Wang Y, Wang N. Highly Efficient Generation of Canker-Resistant Sweet Orange Enabled by an Improved CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2022; 12:769907. [PMID: 35087548 PMCID: PMC8787272 DOI: 10.3389/fpls.2021.769907] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/09/2021] [Indexed: 06/02/2023]
Abstract
Sweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes, and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously [dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, citrus U6 (CsU6) to drive sgRNA expression], we further improved our CRISPR/Cas9 system by choosing superior promoters [Cestrum yellow leaf curling virus (CmYLCV) or Citrus sinensis ubiquitin (CsUbi) promoter] to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker-resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease-resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.
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Savadi S, Mangalassery S, Sandesh MS. Advances in genomics and genome editing for breeding next generation of fruit and nut crops. Genomics 2021; 113:3718-3734. [PMID: 34517092 DOI: 10.1016/j.ygeno.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/21/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India.
| | | | - M S Sandesh
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India
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