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Ningombam L, Hazarika BN, Singh YD, Singh RP, Yumkhaibam T. Aluminium stress tolerance by Citrus plants: a consolidated review. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:705-718. [PMID: 38846464 PMCID: PMC11150227 DOI: 10.1007/s12298-024-01457-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/09/2024]
Abstract
Aluminium, a metallic element abundant in soils as aluminosilicates minerals, poses a toxic threat to plants, particularly in acidic soil conditions, thereby affecting their growth and development. Given their adaptability to diverse soil and climate conditions, Citrus plants have gained significant attention regarding their tolerance to Aluminium toxicity. In the North-eastern region of India, where soils are often slightly acidic with elevated aluminium levels, Citrus species are predominantly found. Understanding the tolerance mechanisms of these Citrus fruits and screening wild Citrus species for their adaptability to abiotic stresses is crucial for enhancing fruit production. Numerous investigations have demonstrated that Citrus species exhibit remarkable tolerance to aluminium contamination, surpassing the typical threshold of 30% incidence. When cultivated in acidic soils, Citrus plants encounter restricted root growth and reduced nutrient and moisture uptake, leading to various nutrient deficiency symptoms. However, promisingly, certain Citrus species such as Citrus jambhiri (Rough lemon), Poncirus trifoliata, Citrus sinensis, and Citrus grandis have shown considerable aluminium tolerance. This comprehensive review delves into the subject of aluminium toxicity and its implications, while also shedding light on the mechanisms through which Citrus plants develop tolerance to this element.
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Affiliation(s)
- Linthoingambi Ningombam
- Department of Fruit Science, College of Horticulture and Forestry, Central Agriculture University, Pasighat, Arunachal Pradesh 791102 India
| | - B. N. Hazarika
- Department of Fruit Science, College of Horticulture and Forestry, Central Agriculture University, Pasighat, Arunachal Pradesh 791102 India
| | - Yengkhom Disco Singh
- Department of Post Harvest Technology, College of Horticulture and Forestry, Central Agriculture University, Pasighat, Arunachal Pradesh 791102 India
| | - Ram Preet Singh
- Department of Fruit Science, College of Horticulture and Forestry, Central Agriculture University, Pasighat, Arunachal Pradesh 791102 India
| | - Tabalique Yumkhaibam
- Department of Vegetable Science, College of Horticulture and Forestry, Central Agriculture University, Pasighat, Arunachal Pradesh 791102 India
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Huang X, Su L, Xian B, Yu Q, Zhang M, Fan J, Zhang C, Liu Y, He H, Zhong X, Li M, Chen S, He Y, Li Q. Genome-wide identification and characterization of the sweet orange (Citrus sinensis) basic helix-loop-helix (bHLH) family reveals a role for CsbHLH085 as a regulator of citrus bacterial canker resistance. Int J Biol Macromol 2024; 267:131442. [PMID: 38621573 DOI: 10.1016/j.ijbiomac.2024.131442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
Citrus bacterial canker (CBC) is a harmful bacterial disease caused by Xanthomonas citri subsp. citri (Xcc), negatively impacting citrus production worldwide. The basic helix-loop-helix (bHLH) transcription factor family plays crucial roles in plant development and stress responses. This study aimed to identify and annotate bHLH proteins encoded in the Citrus sinensis genome and explore their involvement and functional importance in regulating CBC resistance. A total of 135 putative CsbHLHs TFs were identified and categorized into 16 subfamilies. Their chromosomal locations, collinearity, and phylogenetic relationships were comprehensively analyzed. Upon Xcc strain YN1 infection, certain CsbHLHs were differentially regulated in CBC-resistant and CBC-sensitive citrus varieties. Among these, CsbHLH085 was selected for further functional characterization. CsbHLH085 was upregulated in the CBC-resistant citrus variety, was localized in the nucleus, and had a transcriptional activation activity. CsbHLH085 overexpression in Citrus significantly enhanced CBC resistance, accompanied by increased levels of salicylic acid (SA), jasmonic acid (JA), reactive oxygen species (ROS), and decreased levels of abscisic acid (ABA) and antioxidant enzymes. Conversely, CsbHLH085 virus-induced gene silencing resulted in opposite phenotypic and biochemical responses. CsbHLH085 silencing also affected the expression of phytohormone biosynthesis and signaling genes involved in SA, JA, and ABA signaling. These findings highlight the crucial role of CsbHLH085 in regulating CBC resistance, suggesting its potential as a target for biotechnological-assisted breeding citrus varieties with improved resistance against phytopathogens.
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Affiliation(s)
- Xin Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Liyan Su
- School of Biological and Environmental Engineering, Xi'an University, Xi'an 710065, China
| | - Baohang Xian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Qiyuan Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Miao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Jie Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Chenxi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Yiqi Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Houzheng He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Xin Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Man Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Shanchun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China
| | - Yongrui He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China.
| | - Qiang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China.
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Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024; 42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.
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Affiliation(s)
- Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China; Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia 46022, Spain
| | - Li Chao
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Michael G K Jones
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
| | - Hua-Feng Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia.
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Li Q, Xian B, Yu Q, Jia R, Zhang C, Zhong X, Zhang M, Fu Y, Liu Y, He H, Li M, Chen S, He Y. The CsAP2-09-CsWRKY25-CsRBOH2 cascade confers resistance against citrus bacterial canker by regulating ROS homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:534-548. [PMID: 38230828 DOI: 10.1111/tpj.16623] [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: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
Citrus bacterial canker (CBC) is a serious bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that adversely impacts the global citrus industry. In a previous study, we demonstrated that overexpression of an Xcc-inducible apetala 2/ethylene response factor encoded by Citrus sinensis, CsAP2-09, enhances CBC resistance. The mechanism responsible for this effect, however, is not known. In the present study, we showed that CsAP2-09 targeted the promoter of the Xcc-inducible WRKY transcription factor coding gene CsWRKY25 directly, activating its transcription. CsWRKY25 was found to localize to the nucleus and to activate transcriptional activity. Plants overexpressing CsWRKY25 were more resistant to CBC and showed higher expression of the respiratory burst oxidase homolog (RBOH) CsRBOH2, in addition to exhibiting increased RBOH activity. Transient overexpression assays in citrus confirmed that CsWRKY25 and CsRBOH2 participated in the generation of reactive oxygen species (ROS) bursts, which were able to restore the ROS degradation caused by CsAP2-09 knockdown. Moreover, CsWRKY25 was found to bind directly to W-box elements within the CsRBOH2 promoter. Notably, CsRBOH2 knockdown had been reported previously to reduce the CBC resistance, while demonstrated in this study, CsRBOH2 transient overexpression can enhance the CBC resistance. Overall, our results outline a pathway through which CsAP2-09-CsWRKY25 transcriptionally reprograms CsRBOH2-mediated ROS homeostasis in a manner conducive to CBC resistance. These data offer new insight into the mechanisms and regulatory pathways through which CsAP2-09 regulates CBC resistance, highlighting its potential utility as a target for the breeding of CBC-resistant citrus varieties.
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Affiliation(s)
- Qiang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Baohang Xian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Qiyuan Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Ruirui Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Chenxi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Xin Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Miao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Yongyao Fu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Yiqi Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Houzheng He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Man Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Shanchun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Yongrui He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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Huang G, Hu Y, Li F, Zuo X, Wang X, Li F, Li R. Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing. FRONTIERS IN PLANT SCIENCE 2024; 15:1369883. [PMID: 38601304 PMCID: PMC11004388 DOI: 10.3389/fpls.2024.1369883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Introduction Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined. Methods and results In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria. Discussion Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.
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Affiliation(s)
- Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fengyao Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
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Raeisi H, Safarnejad MR, Alavi SM, de Oliveira Andrade M, Farrokhi N, Elahinia SA. Transient expression of anti-HrpE scFv antibody reduces the hypersensitive response in non-host plant against bacterial phytopathogen Xanthomonas citri subsp. citri. Sci Rep 2024; 14:7121. [PMID: 38531981 DOI: 10.1038/s41598-024-57355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Citrus canker is a bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that affects the citrus industry worldwide. Hrp pili subunits (HrpE), an essential component of Type III secretion system (T3SS) bacteria, play a crucial role in the pathogenesis of Xcc by transporting effector proteins into the host cell and causing canker symptoms. Therefore, development of antibodies that block HrpE can suppress disease progression. In this study, a specific scFv detecting HrpE was developed using phage display technique and characterized using sequencing, ELISA, Western blotting, and molecular docking. In addition, a plant expression vector of pCAMBIA-scFvH6 was constructed and agroinfiltrated into Nicotiana tabacum cv. Samson leaves. The hypersensitive response (HR) in the leaves of transformed and non-transformed plants was evaluated by inoculating leaves with Xcc. After three rounds of biopanning of the phage library, a specific human scFv antibody, named scFvH6, was identified that showed high binding activity against HrpE in ELISA and Western blotting. Molecular docking results showed that five intermolecular hydrogen bonds are involved in HrpE-scFvH6 interaction, confirming the specificity and high binding activity of scFvH6. Successful transient expression of pCAMBIA-scFvH6 in tobacco leaves was verified using immunoassay tests. The binding activity of plant-produced scFvH6 to detect HrpE in Western blotting and ELISA was similar to that of bacterial-produced scFvH6 antibody. Interestingly, tobacco plants expressing scFvH6 showed a remarkable reduction in HR induced by Xcc compared with control plants, so that incidence of necrotic lesions was significantly higher in non-transformed controls (≥ 1.5 lesions/cm2) than in the plants producing scFvH6 (≤ 0.5 lesions/cm2) after infiltration with Xcc inoculum. Our results revealed that the expression of scFvH6 in tobacco leaves can confer resistance to Xcc, indicating that this approach could be considered to provide resistance to citrus bacterial canker disease.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran.
| | - Mohammad Reza Safarnejad
- Department of Plant Viruses, Agricultural Research Education and Extension Organization of Iran, Iranian Research Institute of Plant Protection, Tehran, Iran
| | - Seyed Mehdi Alavi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Naser Farrokhi
- Departement of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University G.C, Evin, Tehran, Iran
| | - Seyed Ali Elahinia
- Department of Plant Protection, College of Agricultural Sciences, Guilan University, Rasht, Iran
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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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9
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Fan J, Xian B, Huang X, Yu Q, Zhang M, Zhang C, Jia R, Chen S, He Y, Li Q. Genome-Wide Identification and Characterization of the Sweet Orange ( Citrus sinensis) GATA Family Reveals a Role for CsGATA12 as a Regulator of Citrus Bacterial Canker Resistance. Int J Mol Sci 2024; 25:2924. [PMID: 38474170 DOI: 10.3390/ijms25052924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Citrus bacterial canker (CBC) is a severe bacterial infection caused by Xanthomonas citri subsp. citri (Xcc), which continues to adversely impact citrus production worldwide. Members of the GATA family are important regulators of plant development and regulate plant responses to particular stressors. This report aimed to systematically elucidate the Citrus sinensis genome to identify and annotate genes that encode GATAs and evaluate the functional importance of these CsGATAs as regulators of CBC resistance. In total, 24 CsGATAs were identified and classified into four subfamilies. Furthermore, the phylogenetic relationships, chromosomal locations, collinear relationships, gene structures, and conserved domains for each of these GATA family members were also evaluated. It was observed that Xcc infection induced some CsGATAs, among which CsGATA12 was chosen for further functional validation. CsGATA12 was found to be localized in the nucleus and was differentially upregulated in the CBC-resistant and CBC-sensitive Kumquat and Wanjincheng citrus varieties. When transiently overexpressed, CsGATA12 significantly reduced CBC resistance with a corresponding increase in abscisic acid, jasmonic acid, and antioxidant enzyme levels. These alterations were consistent with lower levels of salicylic acid, ethylene, and reactive oxygen species. Moreover, the bacteria-induced CsGATA12 gene silencing yielded the opposite phenotypic outcomes. This investigation highlights the important role of CsGATA12 in regulating CBC resistance, underscoring its potential utility as a target for breeding citrus varieties with superior phytopathogen resistance.
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Affiliation(s)
- Jie Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Baohang Xian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Xin Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Qiyuan Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Miao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Chenxi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Ruirui Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
- National Citrus Engineering Research Center, Chongqing 400712, China
| | - Shanchun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
- National Citrus Engineering Research Center, Chongqing 400712, China
| | - Yongrui He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
- National Citrus Engineering Research Center, Chongqing 400712, China
| | - Qiang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing 400712, China
- National Citrus Engineering Research Center, Chongqing 400712, China
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10
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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [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: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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11
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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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12
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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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13
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Dong H. Application of genome editing techniques to regulate gene expression in crops. BMC PLANT BIOLOGY 2024; 24:100. [PMID: 38331711 PMCID: PMC10854132 DOI: 10.1186/s12870-024-04786-2] [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: 04/30/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Enhanced agricultural production is urgently required to meet the food demands of the increasing global population. Abundant genetic diversity is expected to accelerate crop development. In particular, the development of the CRISPR/Cas genome editing technology has greatly enhanced our ability to improve crop's genetic diversity through direct artificial gene modification. However, recent studies have shown that most crop improvement efforts using CRISPR/Cas techniques have mainly focused on the coding regions, and there is a relatively lack of studies on the regulatory regions of gene expression. RESULTS This review briefly summarizes the development of CRISPR/Cas system in the beginning. Subsequently, the importance of gene regulatory regions in plants is discussed. The review focuses on recent developments and applications of mutations in regulatory regions via CRISPR/Cas techniques in crop breeding. CONCLUSION Finally, an outline of perspectives for future crop breeding using genome editing technologies is provided. This review provides new research insights for crop improvement using genome editing techniques.
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Affiliation(s)
- Huirong Dong
- College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, 650201, Yunnan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572024, China.
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14
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Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
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Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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15
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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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16
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Santos MG, Nunes da Silva M, Vasconcelos MW, Carvalho SMP. Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker. FRONTIERS IN PLANT SCIENCE 2024; 14:1306420. [PMID: 38273947 PMCID: PMC10808555 DOI: 10.3389/fpls.2023.1306420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.
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Affiliation(s)
- Miguel G. Santos
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
| | - Marta Nunes da Silva
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Susana M. P. Carvalho
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
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17
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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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18
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Xiang W, Guo Z, Han J, Gao Y, Ma F, Gong X. The apple autophagy-related gene MdATG10 improves drought tolerance and water use efficiency in transgenic apple plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108214. [PMID: 38016369 DOI: 10.1016/j.plaphy.2023.108214] [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: 09/06/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
The Loess Plateau is the main apple production area in China; low precipitation is one of the most important factors limiting apple production here. Autophagy is a conserved process in eukaryotes that recycles cell contents or damaged macromolecules. Previously, we identified an autophagy-related gene MdATG10 from apple plants, which was involved in the responses to stressed conditions. In this study, we found that MdATG10 improved the drought tolerance and water use efficiency (WUE) of transgenic apple plants. MdATG10-overexpressing (OE) apple plants were more tolerant of short-term drought stress, as evidenced by their fewer drought-related injuries, compared with wild-type (WT) apple plants. In addition, the WUE of OE plants was higher than that of WT plants under long-term moderate water deficit conditions. The growth rate, biomass accumulation, photosynthetic efficiency, and stomatal aperture were higher in OE plants than in WT plants under long-term moderate drought conditions. During the process of adapting to drought, the expressions of genes involved in the abscisic acid (ABA) pathway were reduced in OE plants to decrease the synthesis of ABA, which helped maintain the stomatal opening for gas exchange. Furthermore, autophagic activity was higher in OE plants than in WT plants, as evidenced by the higher expressions of ATG genes and the greater number of autophagy bodies. In sum, our results suggested that overexpression of MdATG10 improved drought tolerance and WUE in apple plants, possibly by regulating stomatal movement and enhancing autophagic activity, which then enhanced the photosynthetic efficiency and reduced damage, as well as the reactive oxygen species (ROS) accumulation in apple plants.
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Affiliation(s)
- Weijia Xiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zijian Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jifa Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiran Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiaoqing Gong
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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19
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Ntui VO, Tripathi JN, Kariuki SM, Tripathi L. Cassava molecular genetics and genomics for enhanced resistance to diseases and pests. MOLECULAR PLANT PATHOLOGY 2024; 25:e13402. [PMID: 37933591 PMCID: PMC10788594 DOI: 10.1111/mpp.13402] [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: 05/28/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Cassava (Manihot esculenta) is one of the most important sources of dietary calories in the tropics, playing a central role in food and economic security for smallholder farmers. Cassava production is highly constrained by several pests and diseases, mostly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). These diseases cause significant yield losses, affecting food security and the livelihoods of smallholder farmers. Developing resistant varieties is a good way of increasing cassava productivity. Although some levels of resistance have been developed for some of these diseases, there is observed breakdown in resistance for some diseases, such as CMD. A frequent re-evaluation of existing disease resistance traits is required to make sure they are still able to withstand the pressure associated with pest and pathogen evolution. Modern breeding approaches such as genomic-assisted selection in addition to biotechnology techniques like classical genetic engineering or genome editing can accelerate the development of pest- and disease-resistant cassava varieties. This article summarizes current developments and discusses the potential of using molecular genetics and genomics to produce cassava varieties resistant to diseases and pests.
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Affiliation(s)
| | | | | | - Leena Tripathi
- International Institute of Tropical AgricultureNairobiKenya
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20
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Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
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Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
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21
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Yıldırım K, Miladinović D, Sweet J, Akin M, Galović V, Kavas M, Zlatković M, de Andrade E. Genome editing for healthy crops: traits, tools and impacts. FRONTIERS IN PLANT SCIENCE 2023; 14:1231013. [PMID: 37965029 PMCID: PMC10641503 DOI: 10.3389/fpls.2023.1231013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Crop cultivars in commercial use have often been selected because they show high levels of resistance to pathogens. However, widespread cultivation of these crops for many years in the environments favorable to a pathogen requires durable forms of resistance to maintain "healthy crops". Breeding of new varieties tolerant/resistant to biotic stresses by incorporating genetic components related to durable resistance, developing new breeding methods and new active molecules, and improving the Integrated Pest Management strategies have been of great value, but their effectiveness is being challenged by the newly emerging diseases and the rapid change of pathogens due to climatic changes. Genome editing has provided new tools and methods to characterize defense-related genes in crops and improve crop resilience to disease pathogens providing improved food security and future sustainable agricultural systems. In this review, we discuss the principal traits, tools and impacts of utilizing genome editing techniques for achieving of durable resilience and a "healthy plants" concept.
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Affiliation(s)
- Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Ondokuz Mayıs University, Samsun, Türkiye
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jeremy Sweet
- Sweet Environmental Consultants, Cambridge, United Kingdom
| | - Meleksen Akin
- Department of Horticulture, Iğdır University, Iğdır, Türkiye
| | - Vladislava Galović
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Milica Zlatković
- Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Novi Sad, Serbia
| | - Eugenia de Andrade
- National Institute for Agricultural and Veterinary Research (INIAV), I.P., Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
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22
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Jacobson S, Bondarchuk N, Nguyen TA, Canada A, McCord L, Artlip TS, Welser P, Klocko AL. Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple. PLANTS (BASEL, SWITZERLAND) 2023; 12:3693. [PMID: 37960050 PMCID: PMC10649517 DOI: 10.3390/plants12213693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.
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Affiliation(s)
- Seth Jacobson
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Natalie Bondarchuk
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Thy Anh Nguyen
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Allison Canada
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Logan McCord
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Timothy S. Artlip
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Philipp Welser
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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23
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Li H, Song K, Li B, Zhang X, Wang D, Dong S, Yang L. CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis. Int J Mol Sci 2023; 24:15317. [PMID: 37894996 PMCID: PMC10607008 DOI: 10.3390/ijms242015317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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24
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Chen YH, Lu J, Yang X, Huang LC, Zhang CQ, Liu QQ, Li QF. Gene editing of non-coding regulatory DNA and its application in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6158-6175. [PMID: 37549968 DOI: 10.1093/jxb/erad313] [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: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
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Affiliation(s)
- Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xia Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
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25
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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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26
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Aditama R, Tanjung ZA, Aprilyanto V, Sudania WM, Utomo C, Liwang T. Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density. Comput Biol Chem 2023; 106:107931. [PMID: 37481844 DOI: 10.1016/j.compbiolchem.2023.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Transcription control through cis-regulatory elements (CREs) is one of important regulators of gene expression. This study aimed to identify the location of CREs in oil palm (Elaeis guineensis Jacq.) using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). Free energy profiles of each promoter region were calculated using PromPredict software. Raw reads from the deep sequencing of 59 oil palm origins were used to calculate SNP density of each promoter region. The result showed that the average free energy (AFE) on the upstream region of TSS is about 1.5 kcal/mol higher compared to the downstream region. Using DNA free energy method, 16,281 regions of CREs were predicted. Most of predicted CREs was located between 1 and 500 nt upstream of TSS. Anti-correlation pattern between free energy and SNP density was observed on the predicted regions of CREs. This anti-correlated pattern was also observed on an experimentally determined promoter of the oil palm metallothionein gene, EgMSP1. Considering the increasing use of promoter information on plant biotechnology, an easy and accurate promoter prediction using the combination of free energy and SNP density method could be recommended.
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Affiliation(s)
- Redi Aditama
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Zulfikar Achmad Tanjung
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Victor Aprilyanto
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Widyartini Made Sudania
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Condro Utomo
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia.
| | - Tony Liwang
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
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27
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Sabnam N, Hussain A, Saha P. The secret password: Cell death-inducing proteins in filamentous phytopathogens - As versatile tools to develop disease-resistant crops. Microb Pathog 2023; 183:106276. [PMID: 37541554 DOI: 10.1016/j.micpath.2023.106276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Cell death-inducing proteins (CDIPs) are some of the secreted effector proteins manifested by filamentous oomycetes and fungal pathogens to invade the plant tissue and facilitate infection. Along with their involvement in different developmental processes and virulence, CDIPs play a crucial role in plant-pathogen interactions. As the name implies, CDIPs cause necrosis and trigger localised cell death in the infected host tissues by the accumulation of higher concentrations of hydrogen peroxide (H2O2), oxidative burst, accumulation of nitric oxide (NO), and electrolyte leakage. They also stimulate the biosynthesis of defense-related phytohormones such as salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET), as well as the expression of pathogenesis-related (PR) genes that are important in disease resistance. Altogether, the interactions result in the hypersensitive response (HR) in the host plant, which might confer systemic acquired resistance (SAR) in some cases against a vast array of related and unrelated pathogens. The CDIPs, due to their capability of inducing host resistance, are thus unique among the array of proteins secreted by filamentous plant pathogens. More interestingly, a few transgenic plant lines have also been developed expressing the CDIPs with added resistance. Thus, CDIPs have opened an interesting hot area of research. The present study critically reviews the current knowledge of major types of CDIPs identified across filamentous phytopathogens and their modes of action in the last couple of years. This review also highlights the recent breakthrough technologies in studying plant-pathogen interactions as well as crop improvement by enhancing disease resistance through CDIPs.
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Affiliation(s)
- Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India.
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Pallabi Saha
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, United States; Department of Biotechnology, National Institute of Technology, Durgapur, India
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28
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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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Xu L, Mo K, Ran D, Ma J, Zhang L, Sun Y, Long Q, Jiang G, Zhao X, Zou X. An endolysin gene from Candidatus Liberibacter asiaticus confers dual resistance to huanglongbing and citrus canker. HORTICULTURE RESEARCH 2023; 10:uhad159. [PMID: 37719271 PMCID: PMC10500150 DOI: 10.1093/hr/uhad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/27/2023] [Indexed: 09/19/2023]
Abstract
The most damaging citrus diseases are Huanglongbing (HLB) and citrus canker, which are caused by Candidatus Liberibacter asiaticus (CaLas) and Xanthomonas citri pv. citri (Xcc), respectively. Endolysins from bacteriophages are a possible option for disease resistance in plant breeding. Here, we report improvement of citrus resistance to HLB and citrus canker using the LasLYS1 and LasLYS2 endolysins from CaLas. LasLYS2 demonstrated bactericidal efficacy against several Rhizobiaceae bacteria and Xcc, according to inhibition zone analyses. The two genes, driven by a strong promoter from Cauliflower mosaic virus, 35S, were integrated into Carrizo citrange via Agrobacterium-mediated transformation. More than 2 years of greenhouse testing indicated that LasLYS2 provided substantial and long-lasting resistance to HLB, allowing transgenic plants to retain low CaLas titers and no obvious symptoms while also clearing CaLas from infected plants in the long term. LasLYS2 transgenic plants with improved HLB resistance also showed resistance to Xcc, indicating that LasLYS2 had dual resistance to HLB and citrus canker. A microbiome study of transgenic plants revealed that the endolysins repressed Xanthomonadaceae and Rhizobiaceae populations in roots while increasing Burkholderiaceae and Rhodanobacteraceae populations, which might boost the citrus defense response, according to transcriptome analysis. We also found that Lyz domain 2 is the key bactericidal motif of LasLYS1 and LasLYS2. Four endolysins with potential resistance to HLB and citrus canker were found based on the structures of LasLYS1 and LasLYS2. Overall, the work shed light on the mechanisms of resistance of CaLas-derived endolysins, providing insights for designing endolysins to develop broad-spectrum disease resistance in citrus.
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Affiliation(s)
- Lanzhen Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Kaiqing Mo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Danlu Ran
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Juanjuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Lehuan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Yijia Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Qin Long
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Guojin Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Xiaochun Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
| | - Xiuping Zou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing 400712, China
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Liu X, Yu Y, Yao W, Yin Z, Wang Y, Huang Z, Zhou J, Liu J, Lu X, Wang F, Zhang G, Chen G, Xiao Y, Deng H, Tang W. CRISPR/Cas9-mediated simultaneous mutation of three salicylic acid 5-hydroxylase (OsS5H) genes confers broad-spectrum disease resistance in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1873-1886. [PMID: 37323119 PMCID: PMC10440993 DOI: 10.1111/pbi.14099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
Salicylic acid (SA) is an essential plant hormone that plays critical roles in basal defence and amplification of local immune responses and establishes resistance against various pathogens. However, the comprehensive knowledge of the salicylic acid 5-hydroxylase (S5H) in rice-pathogen interaction is still elusive. Here, we reported that three OsS5H homologues displayed salicylic acid 5-hydroxylase activity, converting SA into 2,5-dihydroxybenzoic acid (2,5-DHBA). OsS5H1, OsS5H2, and OsS5H3 were preferentially expressed in rice leaves at heading stage and responded quickly to exogenous SA treatment. We found that bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) strongly induced the expression of OsS5H1, OsS5H2, and OsS5H3. Rice plants overexpressing OsS5H1, OsS5H2, and OsS5H3 showed significantly decreased SA contents and increased 2,5-DHBA levels, and were more susceptible to bacterial blight and rice blast. A simple single guide RNA (sgRNA) was designed to create oss5h1oss5h2oss5h3 triple mutants through CRISPR/Cas9-mediated gene mutagenesis. The oss5h1oss5h2oss5h3 exhibited stronger resistance to Xoo than single oss5h mutants. And oss5h1oss5h2oss5h3 plants displayed enhanced rice blast resistance. The conferred pathogen resistance in oss5h1oss5h2oss5h3 was attributed to the significantly upregulation of OsWRKY45 and pathogenesis-related (PR) genes. Besides, flg22-induced reactive oxygen species (ROS) burst was enhanced in oss5h1oss5h2oss5h3. Collectively, our study provides a fast and effective approach to generate rice varieties with broad-spectrum disease resistance through OsS5H gene editing.
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Affiliation(s)
- Xiong Liu
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Yan Yu
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Wei Yao
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Zhongliang Yin
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Yubo Wang
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Zijian Huang
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Jie‐Qiang Zhou
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Jinling Liu
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Xuedan Lu
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Feng Wang
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Guilian Zhang
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Guihua Chen
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Yunhua Xiao
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Huabing Deng
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
| | - Wenbang Tang
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease ResistanceChangshaChina
- Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
- State Key Laboratory of Hybrid RiceChangshaChina
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Thapliyal G, Bhandari MS, Vemanna RS, Pandey S, Meena RK, Barthwal S. Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield. Crit Rev Biotechnol 2023; 43:884-903. [PMID: 35968912 DOI: 10.1080/07388551.2022.2092714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/27/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
Dangers confronting forest ecosystems are many and the strength of these biological systems is deteriorating, thus substantially affecting tree physiology, phenology, and growth. The establishment of genetically engineered trees into degraded woodlands, which would be adaptive to changing climate, could help in subsiding ecological threats and bring new prospects. This should not be resisted due to the apprehension of transgene dispersal in forests. Consequently, it is important to have a deep insight into the genetic structure and phenotypic limits of the reproductive capability of tree stands/population(s) to endure tolerance and survival. Importantly, for a better understanding of genes and their functional mechanisms, gene editing (GeEd) technology is an excellent molecular tool to unravel adaptation progressions. Therefore, GeEd could be harnessed for resolving the allelic interactions for the creation of gene diversity, and transgene dispersal may be alleviated among the population or species in different bioclimatic zones around the globe. This review highlights the potential of the CRISPR/Cas tools in genomic, transcriptomic, and epigenomic-based assorted and programmable alterations of genes in trees that might be able to fix the trait-specific gene function. Also, we have discussed the application of diverse forms of GeEd to genetically improve several traits, such as wood density, phytochemical constituents, biotic and abiotic stress tolerance, and photosynthetic efficiency in trees. We believe that the technology encourages fundamental research in the forestry sector besides addressing key aspects, which might fasten tree breeding and germplasm improvement programs worldwide.
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Affiliation(s)
- Garima Thapliyal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Ramu S Vemanna
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Forest Protection Division, Forest Research Institute, Dehradun, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
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Shi H, Yang Z, Huang J, Wu H, Fu S, Li W, Zou X, Zhou C, Wang X. An effector of 'Candidatus Liberibacter asiaticus' manipulates autophagy to promote bacterial infection. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4670-4684. [PMID: 37166404 DOI: 10.1093/jxb/erad176] [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: 11/14/2022] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Autophagy functions in plant host immunity responses to pathogen infection. The molecular mechanisms and functions used by the citrus Huanglongbing (HLB)-associated intracellular bacterium 'Candidatus Liberibacter asiaticus' (CLas) to manipulate autophagy are unknown. We identified a CLas effector, SDE4405 (CLIBASIA_04405), which contributes to HLB progression. 'Wanjincheng' orange (Citrus sinensis) transgenic plants expressing SDE4405 promotes CLas proliferation and symptom expression via suppressing host immunity responses. SDE4405 interacts with the ATG8-family of proteins (ATG8s), and their interactions activate autophagy in Nicotiana benthamiana. The occurrence of autophagy is also significantly enhanced in SDE4405-transgenic citrus plants. Interrupting NbATG8s-SDE4405 interaction by silencing of NbATG8c reduces Pseudomonas syringae pv. tomato strain DC3000ΔhopQ1-1 (Pst DC3000ΔhopQ1-1) proliferation in N. benthamiana, and transient overexpression of CsATG8c and SDE4405 in citrus promotes Xanthomonas citri subsp. citri (Xcc) multiplication, suggesting that SDE4405-ATG8s interaction negatively regulates plant defense. These results demonstrate the role of the CLas effector protein in manipulating autophagy, and provide new molecular insights into the interaction between CLas and citrus hosts.
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Affiliation(s)
- Hongwei Shi
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Zuhui Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Jie Huang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Haodi Wu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Shimin Fu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Weimin Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
| | - Xiuping Zou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Changyong Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Xuefeng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [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: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Li Q, Qin X, Zhang M, Yu Q, Jia R, Fan J, Huang X, Fu J, Zhang C, Xian B, Yang W, Long Q, Peng A, Yao L, Chen S, He Y. CsBZIP40 confers resistance against citrus bacterial canker by repressing CsWRKY43-CsPrx53/CsSOD13 cascade mediated ROS scavenging. HORTICULTURE RESEARCH 2023; 10:uhad138. [PMID: 37575655 PMCID: PMC10421728 DOI: 10.1093/hr/uhad138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023]
Abstract
As the bacterial etiologic agent causing citrus bacterial canker (CBC), Xanthomonas citri subsp. citri (Xcc) seriously impacts citrus plantation and fruit production globally. In an earlier study, we demonstrated that CsBZIP40 can positively impact CBC resistance in the sweet orange (Citrus sinensis). However, the mechanistic basis for the protective benefits conferred by CsBZIP40 is yet to be delineated. Here, we show that CsBZIP40 positively regulates CBC resistance and reactive oxygen species (ROS) homeostasis in transgenic sweet orange overexpressing CsBZIP40. CsBZIP40 directly binds to the TGA-box of the CsWRKY43 promoter to repress its transcriptional activity. CsWRKY43 overexpression induces CBC susceptibility in transgenic sweet oranges. In contrast, its inhibition produces strong resistance to CBC. CsWRKY43 directly binds to the W-boxes of the CsPrx53 and CsSOD13 promoters to positively regulate the activities of these antioxidant enzymes, resulting in the negative regulation of ROS homeostasis and CBC resistance in sweet orange plants. CsPrx53/CsSOD13 knockdown enhances ROS accumulation and CBC resistance. Overall, our results outline a regulatory pathway through which CsBZIP40 transcriptionally represses CsWRKY43-CsPrx53/CsSOD13 cascade-mediated ROS scavenging in a manner conducive to CBC resistance. These mechanisms underscore the potential importance of CsBZIP40, CsWRKY43, CsPrx53, and CsSOD13, providing promising strategies for the prevention of CBC.
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Affiliation(s)
- Qiang Li
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
| | - Xiujuan Qin
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Miao Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Qiyuan Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Ruirui Jia
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Jie Fan
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Xin Huang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Jia Fu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Chenxi Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Baohang Xian
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Wen Yang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
| | - Qin Long
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
| | - Aihong Peng
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
| | - Lixiao Yao
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
| | - Shanchun Chen
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
| | - Yongrui He
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing 400712, China
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Erdoğan İ, Cevher-Keskin B, Bilir Ö, Hong Y, Tör M. Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance. BIOLOGY 2023; 12:1037. [PMID: 37508466 PMCID: PMC10376527 DOI: 10.3390/biology12071037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.
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Affiliation(s)
- İbrahim Erdoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Kirsehir Ahi Evran University, Kırşehir 40100, Türkiye
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - Birsen Cevher-Keskin
- Genetic Engineering and Biotechnology Institute, TÜBİTAK Marmara Research Center, Kocaeli 41470, Türkiye
| | - Özlem Bilir
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
- Trakya Agricultural Research Institute, Atatürk Bulvarı 167/A, Edirne 22100, Türkiye
| | - Yiguo Hong
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
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Patel A, Miles A, Strackhouse T, Cook L, Leng S, Patel S, Klinger K, Rudrabhatla S, Potlakayala SD. Methods of crop improvement and applications towards fortifying food security. Front Genome Ed 2023; 5:1171969. [PMID: 37484652 PMCID: PMC10361821 DOI: 10.3389/fgeed.2023.1171969] [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: 02/22/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Agriculture has supported human life from the beginning of civilization, despite a plethora of biotic (pests, pathogens) and abiotic (drought, cold) stressors being exerted on the global food demand. In the past 50 years, the enhanced understanding of cellular and molecular mechanisms in plants has led to novel innovations in biotechnology, resulting in the introduction of desired genes/traits through plant genetic engineering. Targeted genome editing technologies such as Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have emerged as powerful tools for crop improvement. This new CRISPR technology is proving to be an efficient and straightforward process with low cost. It possesses applicability across most plant species, targets multiple genes, and is being used to engineer plant metabolic pathways to create resistance to pathogens and abiotic stressors. These novel genome editing (GE) technologies are poised to meet the UN's sustainable development goals of "zero hunger" and "good human health and wellbeing." These technologies could be more efficient in developing transgenic crops and aid in speeding up the regulatory approvals and risk assessments conducted by the US Departments of Agriculture (USDA), Food and Drug Administration (FDA), and Environmental Protection Agency (EPA).
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Affiliation(s)
- Aayushi Patel
- Penn State Harrisburg, Middletown, PA, United States
| | - Andrew Miles
- Penn State University Park, State College, University Park, PA, United States
| | | | - Logan Cook
- Penn State Harrisburg, Middletown, PA, United States
| | - Sining Leng
- Shanghai United Cell Biotechnology Co Ltd, Shanghai, China
| | - Shrina Patel
- Penn State Harrisburg, Middletown, PA, United States
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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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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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Joshi A, Song HG, Yang SY, Lee JH. Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2454. [PMID: 37447014 DOI: 10.3390/plants12132454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Hyung-Geun Song
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
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40
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Bishnoi R, Kaur S, Sandhu JS, Singla D. Genome engineering of disease susceptibility genes for enhancing resistance in plants. Funct Integr Genomics 2023; 23:207. [PMID: 37338599 DOI: 10.1007/s10142-023-01133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
Introgression of disease resistance genes (R-genes) to fight against an array of phytopathogens takes several years using conventional breeding approaches. Pathogens develop mechanism(s) to escape plants immune system by evolving new strains/races, thus making them susceptible to disease. Conversely, disruption of host susceptibility factors (or S-genes) provides opportunities for resistance breeding in crops. S-genes are often exploited by phytopathogens to promote their growth and infection. Therefore, identification and targeting of disease susceptibility genes (S-genes) are gaining more attention for the acquisition of resistance in plants. Genome engineering of S-genes results in targeted, transgene-free gene modification through CRISPR-Cas-mediated technology and has been reported in several agriculturally important crops. In this review, we discuss the defense mechanism in plants against phytopathogens, tug of war between R-genes and S-genes, in silico techniques for identification of host-target (S-) genes and pathogen effector molecule(s), CRISPR-Cas-mediated S-gene engineering, its applications, challenges, and future prospects.
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Affiliation(s)
- Ritika Bishnoi
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Sehgeet Kaur
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Jagdeep Singh Sandhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
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Ma H, Liu N, Sun X, Zhu M, Mao T, Huang S, Meng X, Li H, Wang M, Liang H. Establishment of an efficient transformation system and its application in regulatory mechanism analysis of biological macromolecules in tea plants. Int J Biol Macromol 2023:125372. [PMID: 37321436 DOI: 10.1016/j.ijbiomac.2023.125372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
Tea (Camellia sinensis), one of the most important beverage crops originated from China and is now cultivated worldwide, provides numerous secondary metabolites that account for its health benefits and rich flavor. However, the lack of an efficient and reliable genetic transformation system has seriously hindered the gene function investigation and precise breeding of C. sinensis. In this study, we established a highly efficient, labor-saving, and cost-effective Agrobacterium rhizogenes-mediated hairy roots genetic transformation system for C. sinensis, which can be used for gene overexpression and genome editing. The established transformation system was simple to operate, bypassing tissue culture and antibiotic screening, and only took two months to complete. We used this system to conduct function analysis of transcription factor CsMYB73 and found that CsMYB73 negatively regulates L-theanine synthesis in tea plant. Additionally, callus formation was successfully induced using transgenic roots, and the transgenic callus exhibited normal chlorophyll production, enabling the study of the corresponding biological functions. Furthermore, this genetic transformation system was effective for multiple C. sinensis varieties and other woody plant species. By overcoming technical obstacles such as low efficiency, long experimental periods, and high costs, this genetic transformation will be a valuable tool for routine gene investigation and precise breeding in tea plants.
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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 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, China.
| | - 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 311300, 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 311300, Zhejiang, China
| | - Mengling Zhu
- 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 311300, Zhejiang, China
| | - Tingfeng Mao
- 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 311300, Zhejiang, 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 311300, 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 311300, Zhejiang, China
| | - Hangfei Li
- 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 311300, 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 311300, Zhejiang, China
| | - Huiling Liang
- 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 311300, Zhejiang, China
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42
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Lee YR, Siddique MI, Kim DS, Lee ES, Han K, Kim SG, Lee HE. CRISPR/Cas9-mediated gene editing to confer turnip mosaic virus (TuMV) resistance in Chinese cabbage ( Brassica rapa). HORTICULTURE RESEARCH 2023; 10:uhad078. [PMID: 37323233 PMCID: PMC10261878 DOI: 10.1093/hr/uhad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Genome editing approaches, particularly the CRISPR/Cas9 technology, are becoming state-of-the-art for trait development in numerous breeding programs. Significant advances in improving plant traits are enabled by this influential tool, especially for disease resistance, compared to traditional breeding. One of the potyviruses, the turnip mosaic virus (TuMV), is the most widespread and damaging virus that infects Brassica spp. worldwide. We generated the targeted mutation at the eIF(iso)4E gene in the TuMV-susceptible cultivar "Seoul" using CRISPR/Cas9 to develop TuMV-resistant Chinese cabbage. We detected several heritable indel mutations in the edited T0 plants and developed T1 through generational progression. It was indicated in the sequence analysis of the eIF(iso)4E-edited T1 plants that the mutations were transferred to succeeding generations. These edited T1 plants conferred resistance to TuMV. It was shown with ELISA analysis the lack of accumulation of viral particles. Furthermore, we found a strong negative correlation (r = -0.938) between TuMV resistance and the genome editing frequency of eIF(iso)4E. Consequently, it was revealed in this study that CRISPR/Cas9 technique can expedite the breeding process to improve traits in Chinese cabbage plants.
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Affiliation(s)
- Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Muhammad Irfan Siddique
- Department of Horticultural Sciences, North Carolina State University Mountain Horticultural Crops Research, Extension Center 455 Research Drive, Mills River, NC 28759, USA
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, 34141, Republic of Korea
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Wang Z, Shea Z, Rosso L, Shang C, Li J, Bewick P, Li Q, Zhao B, Zhang B. Development of new mutant alleles and markers for KTI1 and KTI3 via CRISPR/Cas9-mediated mutagenesis to reduce trypsin inhibitor content and activity in soybean seeds. FRONTIERS IN PLANT SCIENCE 2023; 14:1111680. [PMID: 37223818 PMCID: PMC10200896 DOI: 10.3389/fpls.2023.1111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
The digestibility of soybean meal can be severely impacted by trypsin inhibitor (TI), one of the most abundant anti-nutritional factors present in soybean seeds. TI can restrain the function of trypsin, a critical enzyme that breaks down proteins in the digestive tract. Soybean accessions with low TI content have been identified. However, it is challenging to breed the low TI trait into elite cultivars due to a lack of molecular markers associated with low TI traits. We identified Kunitz trypsin inhibitor 1 (KTI1, Gm01g095000) and KTI3 (Gm08g341500) as two seed-specific TI genes. Mutant kti1 and kti3 alleles carrying small deletions or insertions within the gene open reading frames were created in the soybean cultivar Glycine max cv. Williams 82 (WM82) using the CRISPR/Cas9-mediated genome editing approach. The KTI content and TI activity both remarkably reduced in kti1/3 mutants compared to the WM82 seeds. There was no significant difference in terms of plant growth or maturity days of kti1/3 transgenic and WM82 plants in greenhouse condition. We further identified a T1 line, #5-26, that carried double homozygous kti1/3 mutant alleles, but not the Cas9 transgene. Based on the sequences of kti1/3 mutant alleles in #5-26, we developed markers to co-select for these mutant alleles by using a gel-electrophoresis-free method. The kti1/3 mutant soybean line and associated selection markers will assist in accelerating the introduction of low TI trait into elite soybean cultivars in the future.
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Affiliation(s)
- Zhibo Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Zachary Shea
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Luciana Rosso
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chao Shang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Patrick Bewick
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Qi Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Ijaz M, Khan F, Zaki HEM, Khan MM, Radwan KSA, Jiang Y, Qian J, Ahmed T, Shahid MS, Luo J, Li B. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091911. [PMID: 37176969 PMCID: PMC10180734 DOI: 10.3390/plants12091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.
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Affiliation(s)
- Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250, Australia
| | - Haitham E M Zaki
- Horticulture Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
- Applied Biotechnology Department, University of Technology and Applied Sciences-Sur, Sur 411, Oman
| | - Muhammad Munem Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khlode S A Radwan
- Plant Pathology Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou 311400, China
| | - Jiahui Qian
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod 123, Oman
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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45
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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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46
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Narayanan Z, Glick BR. Biotechnologically Engineered Plants. BIOLOGY 2023; 12:biology12040601. [PMID: 37106801 PMCID: PMC10135915 DOI: 10.3390/biology12040601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023]
Abstract
The development of recombinant DNA technology during the past thirty years has enabled scientists to isolate, characterize, and manipulate a myriad of different animal, bacterial, and plant genes. This has, in turn, led to the commercialization of hundreds of useful products that have significantly improved human health and well-being. Commercially, these products have been mostly produced in bacterial, fungal, or animal cells grown in culture. More recently, scientists have begun to develop a wide range of transgenic plants that produce numerous useful compounds. The perceived advantage of producing foreign compounds in plants is that compared to other methods of producing these compounds, plants seemingly provide a much less expensive means of production. A few plant-produced compounds are already commercially available; however, many more are in the production pipeline.
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Affiliation(s)
- Zareen Narayanan
- Division of Biological Sciences, School of STEM, University of Washington, Bothell, WA 98011, USA
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L3G1, Canada
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Wang J, Wu X, Wang Y, Wu X, Wang B, Lu Z, Li G. Genome-wide characterization and expression analysis of the MLO gene family sheds light on powdery mildew resistance in Lagenaria siceraria. Heliyon 2023; 9:e14624. [PMID: 37025859 PMCID: PMC10070393 DOI: 10.1016/j.heliyon.2023.e14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
MLO (mildew locus O) genes play a vital role in plant disease defense system, especially powdery mildew (PM). Lagenaria siceraria is a distinct Cucurbitaceae crop, and PM is one of the most serious diseases threatening crop production and quality. Although MLOs have been exploited in many Cucurbitaceae species, genome-wide mining of MLO gene family in bottle gourd has not been surveyed yet. Here we identified 16 MLO genes in our recently assembled L. siceraria genome. A total of 343 unique MLO protein sequences from 20 species were characterized and compared to deduce a generally high level of purifying selection and the occurrence of regions related to candidate susceptibility factors in the evolutional divergence. LsMLOs were clustered in six clades containing seven conserved transmembrane domains and 10 clade-specific motifs along with deletion and variation. Three genes (LsMLO3, LsMLO6, and LsMLO13) in clade V showed high sequence identity with orthologues involved in PM susceptibility. The expression pattern of LsMLOs was tissue-specific but not cultivar-specific. Furthermore, it was indicated by qRT-PCR and RNA-seq that LsMLO3 and LsMLO13 were highly upregulated in response to PM stress. Subsequent sequence analysis revealed the structural deletion of LsMLO13 and a single nonsynonymous substitution of LsMLO3 in the PM-resistant genotype. Taken all together, it is speculated that LsMLO13 is likely a major PM susceptibility factor. The results of this study provide new insights into MLO family genes in bottle gourd and find a potential candidate S gene for PM tolerance breeding.
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Du J, Wang Q, Shi H, Zhou C, He J, Wang X. A prophage-encoded effector from "Candidatus Liberibacter asiaticus" targets ASCORBATE PEROXIDASE6 in citrus to facilitate bacterial infection. MOLECULAR PLANT PATHOLOGY 2023; 24:302-316. [PMID: 36692022 PMCID: PMC10013806 DOI: 10.1111/mpp.13296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 05/21/2023]
Abstract
Citrus huanglongbing (HLB), associated with the unculturable phloem-limited bacterium "Candidatus Liberibacter asiaticus" (CLas), is the most devastating disease in the citrus industry worldwide. However, the pathogenicity of CLas remains poorly understood. In this study, we show that AGH17488, a secreted protein encoded by the prophage region of the CLas genome, suppresses plant immunity via targeting the host ASCORBATE PEROXIDASE6 (APX6) protein in Nicotiana benthamiana and Citrus sinensis. The transient expression of AGH17488 reduced the chloroplast localization of APX6 and its enzyme activity, inhibited the accumulation of reactive oxygen species (H2 O2 and O2 - ) and the lipid oxidation endproduct malondialdehyde in plants, and promoted the proliferation of Pseudomonas syringae pv. tomato DC3000 and Xanthomonas citri subsp. citri. This study reveals a novel mechanism underlying how CLas uses a prophage-encoded effector, AGH17488, to target a reactive oxygen species accumulation-related gene, APX6, in the host to facilitate its infection.
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Affiliation(s)
- Jiao Du
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
- Fruit Tree and Melon Information Research CenterZhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesZhengzhouChina
| | - Qiying Wang
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Hongwei Shi
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Jun He
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
| | - Xuefeng Wang
- National Citrus Engineering Research CenterCitrus Research Institute, Southwest UniversityChongqingChina
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Sharma A, Gupta AK, Devi B. Current trends in management of bacterial pathogens infecting plants. Antonie Van Leeuwenhoek 2023; 116:303-326. [PMID: 36683073 DOI: 10.1007/s10482-023-01809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023]
Abstract
Plants are continuously challenged by different pathogenic microbes that reduce the quality and quantity of produce and therefore pose a serious threat to food security. Among them bacterial pathogens are known to cause disease outbreaks with devastating economic losses in temperate, tropical and subtropical regions throughout the world. Bacteria are structurally simple prokaryotic microorganisms and are diverse from a metabolic standpoint. Bacterial infection process mainly involves successful attachment or penetration by using extracellular enzymes, type secretion systems, toxins, growth regulators and by exploiting different molecules that modulate plant defence resulting in successful colonization. Theses bacterial pathogens are extremely difficult to control as they develop resistance to antibiotics. Therefore, attempts are made to search for innovative methods of disease management by the targeting bacterial virulence and manipulating the genes in host plants by exploiting genome editing methods. Here, we review the recent developments in bacterial disease management including the bioactive antimicrobial compounds, bacteriophage therapy, quorum-quenching mediated control, nanoparticles and CRISPR/Cas based genome editing techniques for bacterial disease management. Future research should focus on implementation of smart delivery systems and consumer acceptance of these innovative methods for sustainable disease management.
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Affiliation(s)
- Aditi Sharma
- College of Horticulture and Forestry, Thunag- Mandi, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India.
| | - A K Gupta
- Department of Plant Pathology, Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India
| | - Banita Devi
- Department of Plant Pathology, Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India
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Bhatia S, Pooja, Yadav SK. CRISPR-Cas for genome editing: Classification, mechanism, designing and applications. Int J Biol Macromol 2023; 238:124054. [PMID: 36933595 DOI: 10.1016/j.ijbiomac.2023.124054] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Clustered regularly interspersed short pallindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) came into light as prokaryotic defence mechanism for adaptive immune response. CRISPR-Cas works by integrating short sequences of the target genome (spacers) into the CRISPR locus. The locus containing spacers interspersed repeats is further expressed into small guide CRISPR RNA (crRNA) which is then deployed by the Cas proteins to evade the target genome. Based on the Cas proteins CRISPR-Cas is classified according to polythetic system of classification. The characteristic of the CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new arenas due to which today CRISPR-Cas has evolved as cutting end technique in the field of genome editing. Here, we discuss about the evolution of CRISPR, its classification and various Cas systems including the designing and molecular mechanism of CRISPR-Cas. Applications of CRISPR-Cas as a genome editing tools are also highlighted in the areas such as agriculture, and anticancer therapy. Briefly discuss the role of CRISPR and its Cas systems in the diagnosis of COVID-19 and its possible preventive measures. The challenges in existing CRISP-Cas technologies and their potential solutions are also discussed briefly.
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Affiliation(s)
- Simran Bhatia
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India
| | - Pooja
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India
| | - Sudesh Kumar Yadav
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India.
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