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Xie J, He C, Li Z, Li M, He S, Qian J, Tan B, Zheng X, Cheng J, Wang W, Li J, Feng J, Ye X. A rapid and efficient Agrobacterium-mediated transient transformation system in grape berries. PROTOPLASMA 2024; 261:819-830. [PMID: 38418654 DOI: 10.1007/s00709-024-01938-x] [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: 12/01/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Transient transformation is extremely useful for rapid in vivo assessment of gene function, especially for fruit-related genes. Grape berry, while an important fruit crop, is recalcitrant to transient transformation, due to the high turgor pressure in its mesocarp cells that limits the ability of Agrobacterium to penetrate into the tissue. It is urgent to establish a simple transient transformation system for rapid analysis of gene function. In this study, different injection methods, grape genotypes, and developmental stages were tested in order to develop a rapid and efficient Agrobacterium-mediated transient transformation methodology for grape berries. Two injection methods, namely punch injection and direct injection, were evaluated using the β-glucuronidase (GUS) gene and by x-gluc tissue staining and 4-methylumbelliferyl-β-D-glucuronide fluorescence analysis. The results indicated that there were no significant differences on transformation effects between the two methods, but the latter was more suitable because of its simplicity and convenience. Six grape cultivars ('Hanxiangmi', 'Moldova', 'Zijixin', 'Jumeigui', 'Shine-Muscat', and 'A17') were tested for transient transformation. 'Hanxiangmi', 'Moldova', and 'Zijixin' grape berries were not suitable for agroinfiltration due to frequently fruit cracking, browning, and formation of scar skin. The fruit integrity rates of 'Jumeigui', 'Shine-Muscat', and 'A17' berries were all above 80%, and GUS activity was detected in the berries of the three cultivars 3-14 days after injection with the Agrobacterium culture, while higher GUS activities were observed in the 'Jumeigui' berries. The levels of GUS activity in injected berries at 7-8 weeks after full blooming (WAFB) were more than twice at 6 WAFB. In subsequent assays, the over-expression of MYB transcription factor VvMYB44 via transient transformation accelerated the anthocyanin accumulation and fruit coloring through raising the expression levels of VvLAR1, VvUFGT, VvLDOX, VvANS, and VvDFR, which verified the effectiveness of this transformation system. These experiments finally identified the reliable grape cultivars and suitable operational approach for transient transformation and further indicated that this Agrobacterium-mediated transient transformation system was efficient and suitable for the elucidation of gene function in grape berries.
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Affiliation(s)
- Jiannan Xie
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Chang He
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Zhiqian Li
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Meng Li
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Shanshan He
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Jiakang Qian
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Jidong Li
- College of Forestry, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China.
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China.
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, Henan Province, Zhengzhou, 450002, People's Republic of China.
- International Joint Laboratory of Henan Horticultural Crop Biology, Henan Province, Zhengzhou, 450002, People's Republic of China.
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Tian M, Dai Y, Noman M, Li R, Li X, Wu X, Wang H, Song F, Li D. Genome-wide characterization and functional analysis of the melon TGA gene family in disease resistance through ectopic overexpression in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108784. [PMID: 38823093 DOI: 10.1016/j.plaphy.2024.108784] [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: 09/05/2023] [Revised: 05/11/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
TGA-binding (TGA) transcription factors, characterized by the basic region/leucine zipper motif (bZIP), have been recognized as pivotal regulators in plant growth, development, and stress responses through their binding to the as-1 element. In this study, the TGA gene families in melon, watermelon, cucumber, pumpkin, and zucchini were comprehensively characterized, encompassing analyses of gene/protein structures, phylogenetic relationships, gene duplication events, and cis-acting elements in gene promoters. Upon transient expression in Nicotiana benthamiana, the melon CmTGAs, with typical bZIP and DOG1 domains, were observed to localize within the nucleus. Biochemical investigation revealed specific interactions between CmTGA2/3/5/8/9 and CmNPR3 or CmNPR4. The CmTGA genes exhibited differential expression patterns in melon plants in response to different hormones like salicylic acid, methyl jasmonate, and ethylene, as well as a fungal pathogen, Stagonosporopsis cucurbitacearum that causes gummy stem blight in melon. The overexpression of CmTGA3, CmTGA8, and CmTGA9 in Arabidopsis plants resulted in the upregulation of AtPR1 and AtPR5 expression, thereby imparting enhanced resistance to Pseudomonas syringae pv. Tomato DC3000. In contrast, the overexpression of CmTGA7 or CmTGA9 resulted in a compromised resistance to Botrytis cinerea, coinciding with a concomitant reduction in the expression levels of AtPDF1.2 and AtMYC2 following infection with B. cinerea. These findings shed light on the important roles of specific CmTGA genes in plant immunity, suggesting that genetic manipulation of these genes could be a promising avenue for enhancing plant immune responses.
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Affiliation(s)
- Miao Tian
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yujie Dai
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Muhammad Noman
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ruotong Li
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiaodan Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyi Wu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hui Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Fengming Song
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Dayong Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Yu XN, Guo Y, Yang Q, Yu H, Lu MJ, Zhao L, Jin ZS, Xu XN, Feng JY, Wen YQ. Chimeric mutations in grapevine ENHANCED DISEASE RESISTANCE1 improve resistance to powdery mildew without growth penalty. PLANT PHYSIOLOGY 2024; 195:1995-2015. [PMID: 38507576 DOI: 10.1093/plphys/kiae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Grapevine (Vitis vinifera L.) incurs severe quality degradation and yield loss from powdery mildew, a major fungal disease caused by Erysiphe necator. ENHANCED DISEASE RESISTANCE1 (EDR1), a Raf-like mitogen-activated protein kinase kinase kinase, negatively regulates defense responses against powdery mildew in Arabidopsis (Arabidopsis thaliana). However, little is known about the role of the putatively orthologous EDR1 gene in grapevine. In this study, we obtained grapevine VviEDR1-edited lines using CRISPR/Cas9. Plantlets containing homozygous and bi-allelic indels in VviEDR1 developed leaf lesions shortly after transplanting into the soil and died at the seedling stage. Transgenic plants expressing wild-type VviEDR1 and mutant Vviedr1 alleles as chimera (designated as VviEDR1-chi) developed normally and displayed enhanced resistance to powdery mildew. Interestingly, VviEDR1-chi plants maintained a spatiotemporally distinctive pattern of VviEDR1 mutagenesis: while almost no mutations were detected from terminal buds, ensuring normal function of the apical meristem, mutations occurred in young leaves and increased as leaves matured, resulting in resistance to powdery mildew. Further analysis showed that the resistance observed in VviEDR1-chi plants was associated with callose deposition, increased production of salicylic acid and ethylene, H2O2 production and accumulation, and host cell death. Surprisingly, no growth penalty was observed with VviEDR1-chi plants. Hence, this study demonstrated a role of VviEDR1 in the negative regulation of resistance to powdery mildew in grapevine and provided an avenue for engineering powdery mildew resistance in grapevine.
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Affiliation(s)
- Xue-Na Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Ye Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Qianling Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Haiyan Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Meng-Jiao Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Zhuo-Shuai Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Xiang-Nan Xu
- Institute of Plant Nutrition, Resource and Environment, Beijing Academy of Agriculture and Forestry Sciences, Shuguanghuayuan Mid Road 9, Haidian District, Beijing 100097, China
| | - Jia-Yue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
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Vodiasova E, Sinchenko A, Khvatkov P, Dolgov S. Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine ( Vitis vinifera): New View and Update. Int J Mol Sci 2024; 25:6241. [PMID: 38892428 PMCID: PMC11172563 DOI: 10.3390/ijms25116241] [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: 05/03/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A-E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.
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Affiliation(s)
- Ekaterina Vodiasova
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Anastasiya Sinchenko
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Pavel Khvatkov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Sergey Dolgov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 142290 Puschino, Russia
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Yang Y, Wheatley M, Meakem V, Galarneau E, Gutierrez B, Zhong G. Editing VvDXS1 for the creation of muscat flavour in Vitis vinifera cv. Scarlet Royal. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1610-1621. [PMID: 38243882 PMCID: PMC11123410 DOI: 10.1111/pbi.14290] [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: 09/29/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
Muscat flavour represents a group of unique aromatic attributes in some grape varieties. Biochemically, grape berries with muscat flavour produce high levels of monoterpenes. Monoterpene biosynthesis is mainly through the DOXP/MEP pathway, and VvDXS1 encodes the first enzyme in this plastidial pathway of terpene biosynthesis in grapevine. A single-point mutation resulting in the substitution of a lysine with an asparagine at position 284 in the VvDXS1 protein has previously been identified as the major cause for producing muscat flavour in grapes. In this study, the same substitution in the VvDXS1 protein was successfully created through prime editing in the table grape Vitis vinifera cv. 'Scarlet Royal'. The targeted point mutation was detected in most of the transgenic vines, with varying editing efficiencies. No unintended mutations were detected in the edited alleles, either by PCR Sanger sequencing or by amplicon sequencing. More than a dozen edited vines were identified with an editing efficiency of more than 50%, indicating that these vines were likely derived from single cells in which one allele was edited. These vines had much higher levels of monoterpenes in their leaves than the control, similar to what was found in leaf samples between field-grown muscat and non-muscat grapes.
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Affiliation(s)
- Yingzhen Yang
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Matthew Wheatley
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Victoria Meakem
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Erin Galarneau
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Benjamin Gutierrez
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Gan‐Yuan Zhong
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
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Foresti C, Orduña L, Matus JT, Vandelle E, Danzi D, Bellon O, Tornielli GB, Amato A, Zenoni S. NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2330-2350. [PMID: 38159048 PMCID: PMC11016852 DOI: 10.1093/jxb/erad507] [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: 05/17/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
During late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes involved in berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves resulted in low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61 and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14, the osmotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene WRKY52, and NAC61 itself was validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulatory network that governs stilbenoid metabolism and osmotic, oxidative, and biotic stress responses that are the hallmark of late- and post-ripening grape stages.
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Affiliation(s)
- Chiara Foresti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Davide Danzi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Oscar Bellon
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona, Italy
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Djennane S, Gersch S, Le-Bohec F, Piron MC, Baltenweck R, Lemaire O, Merdinoglu D, Hugueney P, Nogué F, Mestre P. CRISPR/Cas9 editing of Downy mildew resistant 6 (DMR6-1) in grapevine leads to reduced susceptibility to Plasmopara viticola. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2100-2112. [PMID: 38069501 DOI: 10.1093/jxb/erad487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Downy mildew of grapevine (Vitis vinifera), caused by the oomycete Plasmopara viticola, is an important disease that is present in cultivation areas worldwide, and using resistant varieties provides an environmentally friendly alternative to fungicides. DOWNY MILDEW RESISTANT 6 (DMR6) from Arabidopsis is a negative regulator of plant immunity and its loss of function confers resistance to downy mildew. In grapevine, DMR6 is present in two copies, named VvDMR6-1 and VvDMR6-2. Here, we describe the editing of VvDMR6-1 in embryogenic calli using CRISPR/Cas9 and the regeneration of the edited plants. All edited plants were found to be biallelic and chimeric, and whilst they all showed reduced growth compared with non-transformed control plants, they also had reduced susceptibility to P. viticola. Comparison between mock-inoculated genotypes showed that all edited lines presented higher levels of salicylic acid than controls, and lines subjected to transformation presented higher levels of cis-resveratrol than controls. Our results identify VvDMR6-1 as a promising target for breeding grapevine cultivars with improved resistance to downy mildew.
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Affiliation(s)
- Samia Djennane
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | - Sophie Gersch
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | | | | | | | - Olivier Lemaire
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | | | | | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Pere Mestre
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
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8
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Villette J, Lecourieux F, Bastiancig E, Héloir MC, Poinssot B. New improvements in grapevine genome editing: high efficiency biallelic homozygous knock-out from regenerated plantlets by using an optimized zCas9i. PLANT METHODS 2024; 20:45. [PMID: 38500114 PMCID: PMC10949784 DOI: 10.1186/s13007-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND For ten years, CRISPR/cas9 system has become a very useful tool for obtaining site-specific mutations on targeted genes in many plant organisms. This technology opens up a wide range of possibilities for improved plant breeding in the future. In plants, the CRISPR/Cas9 system is mostly used through stable transformation with constructs that allow for the expression of the Cas9 gene and sgRNA. Numerous studies have shown that site-specific mutation efficiency can vary greatly between different plant species due to factors such as plant transformation efficiency, Cas9 expression, Cas9 nucleotide sequence, the addition of intronic sequences, and many other parameters. Since 2016, when the first edited grapevine was created, the number of studies using functional genomic approaches in grapevine has remained low due to difficulties with plant transformation and gene editing efficiency. In this study, we optimized the process to obtain site-specific mutations and generate knock-out mutants of grapevine (Vitis vinifera cv. 'Chardonnay'). Building on existing methods of grapevine transformation, we improved the method for selecting transformed plants at chosen steps of the developing process using fluorescence microscopy. RESULTS By comparison of two different Cas9 gene and two different promoters, we increased site-specific mutation efficiency using a maize-codon optimized Cas9 containing 13 introns (zCas9i), achieving up to 100% biallelic mutation in grapevine plantlets cv. 'Chardonnay'. These results are directly correlated with Cas9 expression level. CONCLUSIONS Taken together, our results highlight a complete methodology for obtaining a wide range of homozygous knock-out mutants for functional genomic studies and future breeding programs in grapevine.
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Affiliation(s)
- Jérémy Villette
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France
| | - Fatma Lecourieux
- UMR1287 EGFV, CNRS, Université de Bordeaux, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, Dijon, France
| | - Eliot Bastiancig
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France
| | | | - Benoit Poinssot
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France.
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9
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Hossain MJ, O’Connor TJ. An efficient and cost-effective method for disrupting genes in RAW264.7 macrophages using CRISPR-Cas9. PLoS One 2024; 19:e0299513. [PMID: 38483963 PMCID: PMC10939251 DOI: 10.1371/journal.pone.0299513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) are widely used for genome editing in cultured cell lines. However, the implementation of genome editing is still challenging due to the complex and often costly multi-step process associated with this technique. Moreover, the efficiency of genome editing varies across cell types, often limiting utility. Herein, we describe pCRISPR-EASY, a vector for simplified cloning of single guide RNAs (sgRNAs) and its simultaneous introduction with CRISPR-Cas9 into cultured cells using a non-viral delivery system. We outline a comprehensive, step-by-step protocol for genome editing in RAW264.7 macrophages, a mouse macrophage cell line widely used in biomedical research for which genome editing using CRISPR-Cas9 has been restricted to lentiviral or expensive commercial reagents. This provides an economical, highly efficient and reliable method for genome editing that can easily be adapted for use in other systems.
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Affiliation(s)
- Mohammad J. Hossain
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Tamara J. O’Connor
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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10
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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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11
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Nor A'azizam NM, Chopra S, Guleria P, Kumar V, Abd Rahim MH, Yaacob JS. Harnessing the potential of mutation breeding, CRISPR genome editing, and beyond for sustainable agriculture. Funct Integr Genomics 2024; 24:44. [PMID: 38421529 DOI: 10.1007/s10142-024-01325-y] [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: 01/05/2024] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
By 2050, the global population is projected to exceed 9.5 billion, posing a formidable challenge to ensure food security worldwide. To address this pressing issue, mutation breeding in horticultural crops, utilizing physical or chemical methods, has emerged as a promising biotechnological strategy. However, the efficacy of these mutagens can be influenced by various factors, including biological and environmental variables, as well as targeted plant materials. This review highlights the global challenges related to food security and explores the potential of mutation breeding as an indispensable biotechnological tool in overcoming food insecurity. This review also covers the emergence of CRISPR-Cas9, a breakthrough technology offering precise genome editing for the development of high-yield, stress-tolerant crops. Together, mutation breeding and CRISPR can potentially address future food demands. This review focuses into these biotechnological advancements, emphasizing their combined potential to fortify global food security in the face of a booming population.
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Affiliation(s)
| | - Sakshi Chopra
- Plant Biotechnology and Genetic Engineering Lab, Department of Biotechnology, DAV University, Jalandhar, Punjab, 144012, India
| | - Praveen Guleria
- Plant Biotechnology and Genetic Engineering Lab, Department of Biotechnology, DAV University, Jalandhar, Punjab, 144012, India
| | - Vineet Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144111, India
| | - Muhamad Hafiz Abd Rahim
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture (CEBAR), Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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12
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [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: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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13
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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14
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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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15
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Zhan Z, Zhang Y, Geng K, Xue X, Deloire A, Li D, Wang Z. Effects of Vine Water Status on Malate Metabolism and γ-Aminobutyric Acid (GABA) Pathway-Related Amino Acids in Marselan ( Vitis vinifera L.) Grape Berries. Foods 2023; 12:4191. [PMID: 38231685 DOI: 10.3390/foods12234191] [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: 10/05/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 01/19/2024] Open
Abstract
Malic acid is the predominant organic acid in grape berries, and its content is affected by abiotic factors such as temperature (fruit zone microclimate) and water (vine water status). The objectives of this study were to explore the potential mechanisms behind the effects of vine water status on the biosynthesis and degradation of berry malic acid and the potential downstream effects on berry metabolism. This study was conducted over two growing seasons in 2021 and 2022, comprising three watering regimes: no water stress (CK), light water stress (LWS), and moderate water stress (MWS). Compared to CK, a significantly higher level of malic acid was found in berries from the MWS treatment when the berry was still hard and green (E-L 33) in both years. However, water stress reduced the malic acid content at the ripe berry harvest (E-L 38) stage. The activities of NAD-malate dehydrogenase (NAD-MDH) and pyruvate kinase (PK) were enhanced by water stress. Except for the E-L 33 stage, the activity of phosphoenolpyruvate carboxylase (PEPC) was reduced by water stress. The highest phosphoenolpyruvate carboxykinase (PEPCK) activity was observed at the berry veraison (E-L 35) stage and coincided with the onset of a decrease in the malate content. Meanwhile, the expression of VvPEPCK was consistent with its enzyme activity. This study showed that water stress changed the content of some free amino acids (GABA, proline, leucine, aspartate, and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway.
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Affiliation(s)
- Zhennan Zhan
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
- Ningxia Wine and Desertifcation Control Vocational and Technical College, Yinchuan 750199, China
| | - Yanxia Zhang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
- Shanxi Academy Agricultural Sciences, Pomology Institute, Shanxi Agricultural University, Taiyuan 030006, China
| | - Kangqi Geng
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaobin Xue
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Alain Deloire
- Department of Biology-Ecology, L'Institut Agro, University of Montpellier, 34060 Montpellier, France
| | - Dongmei Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhenping Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
- School of Agriculture, Ningxia University, Yinchuan 750021, China
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16
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Matinvafa MA, Makani S, Parsasharif N, Zahed MA, Movahed E, Ghiasvand S. CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology. 3 Biotech 2023; 13:383. [PMID: 37920190 PMCID: PMC10618153 DOI: 10.1007/s13205-023-03786-7] [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: 10/29/2022] [Accepted: 09/09/2023] [Indexed: 11/04/2023] Open
Abstract
The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.
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Affiliation(s)
- Mohammad Ali Matinvafa
- Department of Biotechnology & Environment, Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Shadi Makani
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Negin Parsasharif
- Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY USA
| | - Saeedeh Ghiasvand
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Hamedan, Iran
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17
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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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18
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Ren C, Gathunga EK, Li X, Li H, Kong J, Dai Z, Liang Z. Efficient genome editing in grapevine using CRISPR/LbCas12a system. MOLECULAR HORTICULTURE 2023; 3:21. [PMID: 37853418 PMCID: PMC10583370 DOI: 10.1186/s43897-023-00069-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) /Cas12a system, also known as CRISPR/Cpf1, has been successfully harnessed for genome engineering in many plants, but not in grapevine yet. Here we developed and demonstrated the efficacy of CRISPR/Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in inducing targeted mutagenesis by targeting the tonoplastic monosaccharide transporter1 (TMT1) and dihydroflavonol-4-reductase 1 (DFR1) genes in 41B cells. Knockout of DFR1 gene altered flavonoid accumulation in dfr1 mutant cells. Heat treatment (34℃) improved the editing efficiencies of CRISPR/LbCas12a system, and the editing efficiencies of TMT1-crRNA1 and TMT1-crRNA2 increased from 35.3% to 44.6% and 29.9% to 37.3% after heat treatment, respectively. Moreover, the sequences of crRNAs were found to be predominant factor affecting editing efficiencies irrespective of the positions within the crRNA array designed for multiplex genome editing. In addition, genome editing with truncated crRNAs (trucrRNAs) showed that trucrRNAs with 20 nt guide sequences were as effective as original crRNAs with 24 nt guides in generating targeted mutagenesis, whereas trucrRNAs with shorter regions of target complementarity ≤ 18 nt in length may not induce detectable mutations in 41B cells. All these results provide evidence for further applications of CRISPR/LbCas12a system in grapevine as a powerful tool for genome engineering.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Elias Kirabi Gathunga
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xue Li
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Junhua Kong
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China.
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China.
- China National Botanical Garden, Beijing, 100093, PR China.
- Institute of Botany, the Chinese Academy of Sciences, Haidian District, Nanxin Village 20, XiangshanBeijing, 100093, China.
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19
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Zhang Z, Jiang C, Chen C, Su K, Lin H, Zhao Y, Guo Y. VvWRKY5 enhances white rot resistance in grape by promoting the jasmonic acid pathway. HORTICULTURE RESEARCH 2023; 10:uhad172. [PMID: 37841502 PMCID: PMC10569242 DOI: 10.1093/hr/uhad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/20/2023] [Indexed: 10/17/2023]
Abstract
Grape white rot is a disease caused by Coniella diplodiella (Speg.) Sacc. (Cd) can drastically reduce the production and quality of grape (Vitis vinifera). WRKY transcription factors play a vital role in the regulation of plant resistance to pathogens, but their functions in grape white rot need to be further explored. Here, we found that the expression of the WRKY IIe subfamily member VvWRKY5 was highly induced by Cd infection and jasmonic acid (JA) treatment. Transient injection and stable overexpression (in grape calli and Arabidopsis) demonstrated that VvWRKY5 positively regulated grape resistance to white rot. We also determined that VvWRKY5 regulated the JA response by directly binding to the promoters of VvJAZ2 (a JA signaling suppressor) and VvMYC2 (a JA signaling activator), thereby inhibiting and activating the transcription of VvJAZ2 and VvMYC2, respectively. Furthermore, the interaction between VvJAZ2 and VvWRKY5 enhanced the suppression and promotion of VvJAZ2 and VvMYC2 activities by VvWRKY5, respectively. When VvWRKY5 was overexpressed in grape, JA content was also increased. Overall, our results suggested that VvWRKY5 played a key role in regulating JA biosynthesis and signal transduction as well as enhancing white rot resistance in grape. Our results also provide theoretical guidance for the development of elite grape cultivars with enhanced pathogen resistance.
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Affiliation(s)
- Zhen Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
| | - Changyue Jiang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
| | - Cui Chen
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
| | - Kai Su
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
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20
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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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21
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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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22
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Lee MB, Han H, Lee S. The role of WRKY transcription factors, FaWRKY29 and FaWRKY64, for regulating Botrytis fruit rot resistance in strawberry (Fragaria × ananassa Duch.). BMC PLANT BIOLOGY 2023; 23:420. [PMID: 37691125 PMCID: PMC10494375 DOI: 10.1186/s12870-023-04426-1] [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: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND The cultivated strawberry (Fragaria × ananassa Duch.) is one of the most economically important horticultural crops worldwide. Botrytis fruit rot (BFR) caused by the necrotrophic fungal pathogen Botrytis cinerea is the most devasting disease of cultivated strawberries. Most commercially grown strawberry varieties are susceptible to BFR, and controlling BFR relies on repeated applications of various fungicides. Despite extensive efforts, breeding for BFR resistance has been unsuccessful, primarily due to lack of information regarding the mechanisms of disease resistance and genetic resources available in strawberry. RESULTS Using a reverse genetics approach, we identified candidate genes associated with BFR resistance and screened Arabidopsis mutants using strawberry isolates of B. cinerea. Among the five Arabidopsis T-DNA knockout lines tested, the mutant line with AtWRKY53 showed the greatest reduction in disease symptoms of BFR against the pathogen. Two genes, FaWRKY29 and FaWRKY64, were identified as orthologs in the latest octoploid strawberry genome, 'Florida Brilliance'. We performed RNAi-mediated transient assay and found that the disease frequencies were significantly decreased in both FaWRKY29- and FaWRKY64-RNAi fruits of the strawberry cultivar, 'Florida Brilliance'. Furthermore, our transcriptomic data analysis revealed significant regulation of genes associated with ABA and JA signaling, plant cell wall composition, and ROS in FaWRKY29 or FaWRKY64 knockdown strawberry fruits in response to the pathogen. CONCLUSION Our study uncovered the foundational role of WRKY transcription factor genes, FaWRKY29 and FaWRKY64, in conferring resistance against B. cinerea. The discovery of susceptibility genes involved in BFR presents significant potential for developing resistance breeding strategies in cultivated strawberries, potentially leveraging CRISPR-based gene editing techniques.
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Affiliation(s)
- Man Bo Lee
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Korea
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA
| | - Hyeondae Han
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA.
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23
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Nguyen TT, Pham DT, Nguyen NH, Do PT, To HTM. The Germin-like protein gene OsGER4 is involved in heat stress response in rice root development. Funct Integr Genomics 2023; 23:271. [PMID: 37561192 DOI: 10.1007/s10142-023-01201-1] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important dietary carbohydrate sources for half of the world's population. However, it is not well adapted to environmental stress conditions, necessitating to create new and improved varieties to help ensure sufficient rice production in the face of rising populations and shrinking arable land. Recently, the development of the CRISPR/Cas9 gene editing system has allowed researchers to study functional genomics and engineer new rice varieties with great efficiency compared to conventional methods. In this study, we investigate the involvement of OsGER4, a germin-like protein identified by a genome-wide association study that is associated with rice root development under a stress hormone jasmonic acids treatment. Analysis of the OsGER4 promoter region revealed a series of regulatory elements that connect this gene to ABA signaling and water stress response. Under heat stress, osger4 mutant lines produce a significantly lower crown root than wild-type Kitaake rice. The loss of OsGER4 also led to the reduction of lateral root development. Using the GUS promoter line, OsGER4 expression was detected in the epidermis of the crown root primordial, in the stele of the crown root, and subsequently in the primordial of the lateral root. Taken together, these results illustrated the involvement of OsGER4 in root development under heat stress by regulating auxin transport through plasmodesmata, under control by both ABA and auxin signaling.
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Affiliation(s)
- Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Dan The Pham
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Nhung Hong Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam.
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24
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Ali A, Zafar MM, Farooq Z, Ahmed SR, Ijaz A, Anwar Z, Abbas H, Tariq MS, Tariq H, Mustafa M, Bajwa MH, Shaukat F, Razzaq A, Maozhi R. Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnol J 2023; 18:e2200642. [PMID: 37166088 DOI: 10.1002/biot.202200642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.
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Affiliation(s)
- Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | | | - Zunaira Farooq
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Huma Abbas
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Hala Tariq
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mahwish Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Fiza Shaukat
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdul Razzaq
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ren Maozhi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of, Urban Agriculture, Chinese Academy of Agriculture Science, Chengdu, China
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25
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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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26
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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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27
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Nakajima I, Kawahigashi H, Nishitani C, Azuma A, Haji T, Toki S, Endo M. Targeted deletion of grape retrotransposon associated with fruit skin color via CRISPR/Cas9 in Vitis labrascana 'Shine Muscat'. PLoS One 2023; 18:e0286698. [PMID: 37289779 PMCID: PMC10249860 DOI: 10.1371/journal.pone.0286698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Transposition of transposable elements affect expression levels, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus. For example, in grape, presence of the Gret1 retrotransposon in the promoter region of the VvMYBA1a allele at the VvMYBA1 locus suppress the expression of the VvMYBA1 transcription factor gene for the anthocyanin biosynthesis and this transposon insertion is responsible for the green berry skin color of Vitis labrascana, 'Shine Muscat', a major grape cultivar in Japan. To prove that transposons in grape genome can be removed by genome editing, we focused on Gret1 in the VvMYBA1a allele as a target of CRISPR/Cas9 mediated transposon removal. PCR amplification and sequencing detected Gret1 eliminated cells in 19 of 45 transgenic plants. Although we have not yet confirmed any effects on grape berry skin color, we were successful in demonstrating that cleaving the long terminal repeat (LTR) present at both ends of Gret1 can efficiently eliminate the transposon.
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Affiliation(s)
- Ikuko Nakajima
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroyuki Kawahigashi
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chikako Nishitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Akifumi Azuma
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi Haji
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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28
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Pei MS, Liu HN, Ampomah-Dwamena C, Wei TL, Yu YH, Jiao JB, Lv YY, Li F, Li HC, Zhu XJ, Guo DL. A simple and efficient protocol for transient transformation of sliced grape berries. PROTOPLASMA 2023; 260:757-766. [PMID: 36089607 DOI: 10.1007/s00709-022-01810-w] [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: 06/23/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Grape is an economically important crop but recalcitrant to Agrobacterium-mediated genetic transformation and in vitro regeneration. Here, we have developed a protocol for transient transformation of grapes by investigating the effects of explant pre-culture and duration of vacuum infiltration on transformation efficiency. Using sliced grape berries of "Shine-Muscat" (Vitis labrusca × Vitis vinifera) between the end of fruit expansion phase and the mature stage as explants, we firstly compared the effect of pre-culture explants into a susceptible state (incubation on Murashige and Skoog (MS) agar plate in the dark at 25 ± 1 °C for 48 h) with no pre-culture and then tested different vacuum infiltration times on transformation efficiency using β-glucuronidase (GUS) reporter system. Pre-culture increased the susceptibility of explants to the agrobacteria infection and increased transient transformation efficiency as assessed by histochemical GUS activity, with intense blue coloration compared with the faint staining observed in the non-susceptible explants. Using a Circulating Water Vacuum Pump system to facilitate agrobacteria entry into berry cells, we tested vacuum durations of 5, 10, and 15 min and observed that transformation efficiency increased with vacuum duration of infiltration. These results were confirmed by relative gene expression of GUS transgene as assessed by RT-qPCR and GUS activity assay. To further confirm the usefulness of our protocol, we transiently transformed grape berries with the hydrogen peroxide sensor gene VvHPCA3, and this was confirmed by gene expression analysis as well as increased sensitivity of the explants to hydrogen peroxide treatment. Overall, this study has resulted in a simple but efficient transient transformation protocol for grape berries and would be a valuable tool for the rapid testing of gene function and the study of key regulatory networks in this important crop.
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Affiliation(s)
- Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | | | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | - Jia-Bing Jiao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | - Ying-Ying Lv
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China
| | - Feng Li
- Yanqing District Fruit Industry Service Station, Beijing, People's Republic of China
| | - Hong-Chao Li
- Forestry Development Centre of Xiangfu District, Kaifeng, People's Republic of China
| | - Xue-Jie Zhu
- Nong Fa Agricultural Science and Technology Company Limited, Luoyang, People's Republic of China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, People's Republic of China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, People's Republic of China.
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Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I. An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics 2023; 23:119. [PMID: 37022538 DOI: 10.1007/s10142-023-01036-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.
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Affiliation(s)
- Muhammad Sufyan
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Umar Daraz
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Sajjad Hyder
- Department of Botant, Government College Women University, Sialkot, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo, 11835, Egypt
| | - Farzana Rafiq
- School of Environmental Sciences and Engineering, NCEPU, Beijing, China
| | - Naveed Mahmood
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Khurram Shahzad
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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30
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Boubakri H. Recent progress in CRISPR/Cas9-based genome editing for enhancing plant disease resistance. Gene 2023; 866:147334. [PMID: 36871676 DOI: 10.1016/j.gene.2023.147334] [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: 07/20/2022] [Revised: 12/22/2022] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Nowadays, agricultural production is strongly affected by both climate change and pathogen attacks which seriously threaten global food security. For a long time, researchers have been waiting for a tool allowing DNA/RNA manipulation to tailor genes and their expression. Some earlier genetic manipulation methods such as meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) allowed site directed modification but their successful rate was limited due to lack of flexibility when targeting a 'site-specific nucleic acid'. The discovery of clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has revolutionized genome editing domain in different living organisms during the past 9 years. Based on RNA-guided DNA/RNA recognition, CRISPR/Cas9 optimizations have offered an unrecorded scientific opportunity to engineer plants resistant to diverse pathogens. In this report, we describe the main characteristics of the primary reported-genome editing tools ((MNs, ZFNs, TALENs) and evaluate the different CRISPR/Cas9 methods and achievements in developing crop plants resistant to viruses, fungi and bacteria.
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Affiliation(s)
- Hatem Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia.
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31
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Su K, Zhao W, Lin H, Jiang C, Zhao Y, Guo Y. Candidate gene discovery of Botrytis cinerea resistance in grapevine based on QTL mapping and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1127206. [PMID: 36824203 PMCID: PMC9941706 DOI: 10.3389/fpls.2023.1127206] [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: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Grape gray mold disease (Botrytis cinerea) is widespread during grape production especially in Vitis vinifera and causes enormous losses to the grape industry. In nature, the grapevine cultivar 'Beta ' (Vitis riparia × Vitis labrusca) showed high resistance to grape gray mold. Until now, the candidate genes and their mechanism of gray mold resistance were poorly understood. In this study, we firstly conducted quantitative trait locus (QTL) mapping for grape gray mold resistance based on two hybrid offspring populations that showed wide separation in gray mold resistance. Notably, two stable QTL related to gray mold resistance were detected and located on linkage groups LG2 and LG7. The phenotypic variance ranged from 6.86% to 13.70% on LG2 and 4.40% to 11.40% on LG7. Combined with RNA sequencing (RNA-seq), one structural gene VlEDR2 (Vitvi02g00982) and three transcription factors VlERF039 (Vitvi00g00859), VlNAC047 (Vitvi08g01843), and VlWRKY51 (Vitvi07g01847) that may be involved in VlEDR2 expression and grape gray mold resistance were selected. This discovery of candidate gray mold resistance genes will provide an important theoretical reference for grape gray mold resistance mechanisms, research, and gray mold-resistant grape cultivar breeding in the future.
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Affiliation(s)
- Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, China
| | - Wei Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Changyue Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, China
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32
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Dong BR, Jiang R, Chen JF, Xiao Y, Lv ZY, Chen WS. Strategic nanoparticle-mediated plant disease resistance. Crit Rev Biotechnol 2023; 43:22-37. [PMID: 35282729 DOI: 10.1080/07388551.2021.2007842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanotechnology is a promising means for development of sustainable agriculture while the study of nanoparticle-mediated plant disease resistance is still in its primary stage. Nanotechnology has shown great promise in regulating: the content of secondary metabolites, inducing disease resistance genes, delivering hormones, delivering biomolecules (such as: nucleotides, proteins, and activators), and obtaining transgenic plants to resist plant diseases. In this review, we conclude its versatility and applicability in disease management strategies and diagnostics and as molecular tools. With the advent of new biotechnologies (e.g. de novo regeneration, CRISPR/Cas9, and GRF4-GIF1 fusion protein), we discuss the potential of nanoparticles as an optimal platform to deliver biomolecules to plants for genetic engineering. In order to ensure the safe use and social acceptance of plant nanoparticle technology, its adverse effects are discussed, including the risk of transferring nanoparticles through the food chain.
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Affiliation(s)
- Bo-Ran Dong
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rui Jiang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jun-Feng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zong-You Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wan-Sheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
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He F, Wang C, Sun H, Tian S, Zhao G, Liu C, Wan C, Guo J, Huang X, Zhan G, Yu X, Kang Z, Guo J. Simultaneous editing of three homoeologues of TaCIPK14 confers broad-spectrum resistance to stripe rust in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:354-368. [PMID: 36326663 PMCID: PMC9884018 DOI: 10.1111/pbi.13956] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 10/25/2022] [Accepted: 11/01/2022] [Indexed: 05/26/2023]
Abstract
Wheat stripe rust caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive wheat diseases resulting in significant losses to wheat production worldwide. The development of disease-resistant varieties is the most economical and effective measure to control diseases. Altering the susceptibility genes that promote pathogen compatibility via CRISPR/Cas9-mediated gene editing technology has become a new strategy for developing disease-resistant wheat varieties. Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) has been demonstrated to be involved in defence responses during plant-pathogen interactions. However, whether wheat CIPK functions as susceptibility factor is still unclear. Here, we isolated a CIPK homoeologue gene TaCIPK14 from wheat. Knockdown of TaCIPK14 significantly increased wheat resistance to Pst, whereas overexpression of TaCIPK14 resulted in enhanced wheat susceptibility to Pst by decreasing different aspects of the defence response, including accumulation of ROS and expression of pathogenesis-relative genes. We generated wheat Tacipk14 mutant plants by simultaneous modification of the three homoeologues of wheat TaCIPK14 via CRISPR/Cas9 technology. The Tacipk14 mutant lines expressed race-nonspecific (RNS) broad-spectrum resistance (BSR) to Pst. Moreover, no significant difference was found in agronomic yield traits between Tacipk14 mutant plants and Fielder control plants under greenhouse and field conditions. These results demonstrate that TaCIPK14 acts as an important susceptibility factor in wheat response to Pst, and knockout of TaCIPK14 represents a powerful strategy for generating new disease-resistant wheat varieties with BSR to Pst.
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Affiliation(s)
- Fuxin He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Ce Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Huilin Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Shuxin Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Guosen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Cuiping Wan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Xueling Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiumei Yu
- Technological Innovation Centre for Biological Control of Crop Diseases and Insect Pests of Hebei ProvinceHebei Agricultural UniversityBaodingHebeiChina
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
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34
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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35
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Nerva L, Dalla Costa L, Ciacciulli A, Sabbadini S, Pavese V, Dondini L, Vendramin E, Caboni E, Perrone I, Moglia A, Zenoni S, Michelotti V, Micali S, La Malfa S, Gentile A, Tartarini S, Mezzetti B, Botta R, Verde I, Velasco R, Malnoy MA, Licciardello C. The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives. Int J Mol Sci 2023; 24:ijms24020977. [PMID: 36674493 PMCID: PMC9861864 DOI: 10.3390/ijms24020977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023] Open
Abstract
Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.
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Affiliation(s)
- Luca Nerva
- Research Center for Viticulture and Enology, Council for Agricultural Research and Economics, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all’Adige, Italy
| | - Angelo Ciacciulli
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Vera Pavese
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Luca Dondini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elisa Vendramin
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Emilia Caboni
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Vania Michelotti
- Research Center for Genomics and Bioinformatics, Council for Agricultural Research and Economics, 29017 Fiorenzuola D’Arda, Italy
| | - Sabrina Micali
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Stefano La Malfa
- Department of Biotechnology, University of Catania, 95124 Catania, Italy
| | - Alessandra Gentile
- Department of Biotechnology, University of Catania, 95124 Catania, Italy
| | - Stefano Tartarini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Bruno Mezzetti
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Roberto Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
| | - Ignazio Verde
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 00134 Rome, Italy
| | - Riccardo Velasco
- Research Center for Viticulture and Enology, Council for Agricultural Research and Economics, 31015 Conegliano, Italy
| | - Mickael Arnaud Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all’Adige, Italy
- Correspondence: (M.A.M.); (C.L.); Tel.: +39-04-6161-5536 (M.A.M.); +39-09-5765-3104 (C.L.)
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
- Correspondence: (M.A.M.); (C.L.); Tel.: +39-04-6161-5536 (M.A.M.); +39-09-5765-3104 (C.L.)
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Najafi S, Bertini E, D’Incà E, Fasoli M, Zenoni S. DNA-free genome editing in grapevine using CRISPR/Cas9 ribonucleoprotein complexes followed by protoplast regeneration. HORTICULTURE RESEARCH 2023; 10:uhac240. [PMID: 37077374 PMCID: PMC10108004 DOI: 10.1093/hr/uhac240] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/17/2022] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas9 genome editing technology can overcome many limitations of traditional breeding, offering enormous potential for crop improvement and food production. Although the direct delivery of Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) complexes to grapevine (Vitis vinifera) protoplasts has been shown before, the regeneration of edited protoplasts into whole plants has not been reported. Here, we describe an efficient approach to obtain transgene-free edited grapevine plants by the transfection and subsequent regeneration of protoplasts isolated from embryogenic callus. As proof of concept, a single-copy green fluorescent protein reporter gene (GFP) in the grapevine cultivar Thompson Seedless was targeted and knocked out by the direct delivery of RNPs to protoplasts. CRISPR/Cas9 activity, guided by two independent sgRNAs, was confirmed by the loss of GFP fluorescence. The regeneration of GFP- protoplasts into whole plants was monitored throughout development, confirming that the edited grapevine plants were comparable in morphology and growth habit to wild-type controls. We report the first highly efficient protocol for DNA-free genome editing in grapevine by the direct delivery of preassembled Cas9-sgRNA RNP complexes into protoplasts, helping to address the regulatory concerns related to genetically modified plants. This technology could encourage the application of genome editing for the genetic improvement of grapevine and other woody crop plants.
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Affiliation(s)
- Samaneh Najafi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Edoardo Bertini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Erica D’Incà
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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Sharma P, Pandey A, Malviya R, Dey S, Karmakar S, Gayen D. Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals. Front Genome Ed 2023; 5:1094965. [PMID: 36911238 PMCID: PMC9998953 DOI: 10.3389/fgeed.2023.1094965] [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: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Agricultural production relies on horticultural crops, including vegetables, fruits, and ornamental plants, which sustain human life. With an alarming increase in human population and the consequential need for more food, it has become necessary for increased production to maintain food security. Conventional breeding has subsidized the development of improved verities but to enhance crop production, new breeding techniques need to be acquired. CRISPR-Cas9 system is a unique and powerful genome manipulation tool that can change the DNA in a precise way. Based on the bacterial adaptive immune system, this technique uses an endonuclease that creates double-stranded breaks (DSBs) at the target loci under the guidance of a single guide RNA. These DSBs can be repaired by a cellular repair mechanism that installs small insertion and deletion (indels) at the cut sites. When equated to alternate editing tools like ZFN, TALENs, and meganucleases, CRISPR- The cas-based editing tool has quickly gained fast-forward for its simplicity, ease to use, and low off-target effect. In numerous horticultural and industrial crops, the CRISPR technology has been successfully used to enhance stress tolerance, self-life, nutritional improvements, flavor, and metabolites. The CRISPR-based tool is the most appropriate one with the prospective goal of generating non-transgenic yields and avoiding the regulatory hurdles to release the modified crops into the market. Although several challenges for editing horticultural, industrial, and ornamental crops remain, this new novel nuclease, with its crop-specific application, makes it a dynamic tool for crop improvement.
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Affiliation(s)
- Punam Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | | | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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38
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Vaia G, Pavese V, Moglia A, Cristofori V, Silvestri C. Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry. FRONTIERS IN PLANT SCIENCE 2022; 13:1074541. [PMID: 36589127 PMCID: PMC9800005 DOI: 10.3389/fpls.2022.1074541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Among the New Plant Breeding Techniques (NPBTs), the CRISPR/Cas9 system represents a useful tool for target gene editing, improving the traits of the plants rapidly. This technology allows targeting one or more sequences simultaneously, as well as introducing new genetic variations by homology-directed recombination. However, the technology of CRISPR/Cas9 remains a challenge for some polyploid woody species, since all the different alleles for which the mutation is required must be simultaneously targeted. In this work we describe improved protocols adapting the CRISPR/Cas9 system to highbush blueberry (Vaccinium corymbosum L.), using Agrobacterium-mediated transformation. As a proof of concept, we targeted the gene encoding for phytoene desaturase, whose mutation disrupts chlorophyll biosynthesis allowing for the visual assessment of knockout efficiency. Leaf explants of in vitro-cultured blueberry cv. Berkeley has been transformed with a CRISPR/Cas9 construct containing two guide RNAs (gRNA1 and gRNA2) targeting two conserved gene regions of pds and subsequently maintained on a selection medium enriched with kanamycin. After 4 weeks in culture on the selection medium, the kanamycin-resistant lines were isolated, and the genotyping of these lines through Sanger sequencing revealed successful gene editing. Some of mutant shoot lines included albino phenotypes, even if the editing efficiencies were quite low for both gRNAs, ranging between 2.1 and 9.6% for gRNA1 and 3.0 and 23.8 for gRNA2. Here we showed a very effective adventitious shoot regeneration protocol for the commercial cultivar of highbush blueberry "Berkeley", and a further improvement in the use of CRISPR/Cas9 system in Vaccinium corymbosum L., opening the way to the breeding mediated by biotechnological approaches.
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Affiliation(s)
- Giuseppe Vaia
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Valerio Cristofori
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Cristian Silvestri
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università della Tuscia, Viterbo, Italy
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39
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Shcherban AB. Plant genome modification: from induced mutagenesis to genome editing. Vavilovskii Zhurnal Genet Selektsii 2022; 26:684-696. [DOI: 10.18699/vjgb-22-83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- A. B. Shcherban
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS
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Liu H, Lin B, Ren Y, Hao P, Huang L, Xue B, Jiang L, Zhu Y, Hua S. CRISPR/Cas9-mediated editing of double loci of BnFAD2 increased the seed oleic acid content of rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1034215. [PMID: 36483970 PMCID: PMC9723152 DOI: 10.3389/fpls.2022.1034215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Seed oleic acid is an important quality trait sought in rapeseed breeding programs. Many methods exist to increase seed oleic acid content, such as the CRISPR/Cas9-mediated genome editing system, yet there is no report on seed oleic acid content improvement via this system's precise editing of the double loci of BnFAD2. Here, a precise CRISPR/Cas9-mediated genome editing of the encoded double loci (A5 and C5) of BnFAD2 was established. The results demonstrated high efficiency of regeneration and transformation, with the rapeseed genotype screened in ratios of 20.18% and 85.46%, respectively. The total editing efficiency was 64.35%, whereas the single locus- and double locus-edited ratios were 21.58% and 78.42%, respectively. The relative proportion of oleic acid with other fatty acids in seed oil of mutants was significantly higher for those that underwent the editing on A5 copy than that on C5 copy, but it was still less than 80%. For double locus-edited mutants, their relative proportion of oleic acid was more than 85% in the T1 and T4 generations. A comparison of the sequences between the double locus-edited mutants and reference showed that no transgenic border sequences were detected from the transformed vector. Analysis of the BnFAD2 sequence on A5 and C5 at the mutated locus of double loci mutants uncovered evidence for base deletion and insertion, and combination. Further, no editing issue of FAD2 on the copy of A1 was detected on the three targeted editing regions. Seed yield, yield component, oil content, and relative proportion of oleic acid between one selected double loci-edited mutant and wild type were also compared. These results showed that although the number of siliques per plant of the wild type was significantly higher than those of the mutant, the differences in seed yield and oil content were not significant between them, albeit with the mutant having a markedly higher relative proportion of oleic acid. Altogether, our results confirmed that the established CRISPR/Cas9-mediated genome editing of double loci (A5 and C5) of the BnFAD2 can precisely edit the targeted genes, thereby enhancing the seed oleic acid content to a far greater extent than can a single locus-editing system.
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Affiliation(s)
- Han Liu
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Department of Seed Management, Yongding Agriculture and Rural Bureau of Longyan, Longyan, China
| | - Baogang Lin
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yun Ren
- Huzhou Agricultural Science and Technology Development Center, Institution of Crop Science, Huzhou, China
| | - Pengfei Hao
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Lan Huang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Bowen Xue
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Lixi Jiang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
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41
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Transgenic Improvement for Biotic Resistance of Crops. Int J Mol Sci 2022; 23:ijms232214370. [PMID: 36430848 PMCID: PMC9697442 DOI: 10.3390/ijms232214370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Biotic constraints, including pathogenic fungi, viruses and bacteria, herbivory insects, as well as parasitic nematodes, cause significant yield loss and quality deterioration of crops. The effect of conventional management of these biotic constraints is limited. The advances in transgenic technologies provide a direct and directional approach to improve crops for biotic resistance. More than a hundred transgenic events and hundreds of cultivars resistant to herbivory insects, pathogenic viruses, and fungi have been developed by the heterologous expression of exogenous genes and RNAi, authorized for cultivation and market, and resulted in a significant reduction in yield loss and quality deterioration. However, the exploration of transgenic improvement for resistance to bacteria and nematodes by overexpression of endogenous genes and RNAi remains at the testing stage. Recent advances in RNAi and CRISPR/Cas technologies open up possibilities to improve the resistance of crops to pathogenic bacteria and plant parasitic nematodes, as well as other biotic constraints.
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Kalaitzandonakes N, Willig C, Zahringer K. The economics and policy of genome editing in crop improvement. THE PLANT GENOME 2022:e20248. [PMID: 36321718 DOI: 10.1002/tpg2.20248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
In this review article we analyze the economics of genome editing and its potential long-term effect on crop improvement and agriculture. We describe the emergence of genome editing as a novel platform for crop improvement, distinct from the existing platforms of plant breeding and genetic engineering. We review key technical characteristics of genome editing and describe how it enables faster trait development, lower research and development costs, and the development of novel traits not possible through previous crop improvement methods. Given these fundamental technical and economic advantages, we describe how genome editing can greatly increase the productivity and broaden the scope of crop improvement with potential outsized economic effects. We further discuss how the global regulatory policy environment, which is still emerging, can shape the ultimate path of genome editing innovation, its effect on crop improvement, and its overall socioeconomic benefits to society.
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Affiliation(s)
| | | | - Kenneth Zahringer
- Division of Applied Social Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
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Töpfer R, Trapp O. A cool climate perspective on grapevine breeding: climate change and sustainability are driving forces for changing varieties in a traditional market. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3947-3960. [PMID: 35389053 PMCID: PMC9729149 DOI: 10.1007/s00122-022-04077-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
A multitude of diverse breeding goals need to be combined in a new cultivar, which always forces to compromise. The biggest challenge grapevine breeders face is the extraordinarily complex trait of wine quality, which is the all-pervasive and most debated characteristic. Since the 1920s, Germany runs continuous grapevine breeding programmes. This continuity was the key to success and lead to various new cultivars on the market, so called PIWIs. Initially, introduced pests and diseases such as phylloxera, powdery and downy mildew were the driving forces for breeding. However, preconceptions about the wine quality of new resistant selections impeded the market introduction. These preconceptions are still echoing today and may be the reason in large parts of the viticultural community for: (1) ignoring substantial breeding progress, and (2) sticking to successful markets of well-known varietal wines or blends (e.g. Chardonnay, Cabernet Sauvignon, Riesling). New is the need to improve viticulture´s sustainability and to adapt to changing environmental conditions. Climate change with its extreme weather will impose the need for a change in cultivars in many wine growing regions. Therefore, a paradigm shift is knocking on the door: new varieties (PIWIs) versus traditional varieties for climate adapted and sustainable viticulture. However, it will be slow process and viticulture is politically well advised to pave the way to variety innovation. In contrast to the widely available PIWIs, competitive cultivars created by means of new breeding technologies (NBT, e.g. through CRISPR/Cas) are still decades from introduction to the market.
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Affiliation(s)
- Reinhard Töpfer
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany.
| | - Oliver Trapp
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
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Multiplex CRISPR/Cas9-mediated knockout of the phytoene desaturase gene in Coffea canephora. Sci Rep 2022; 12:17270. [PMID: 36241651 PMCID: PMC9568650 DOI: 10.1038/s41598-022-21566-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
Coffea canephora (2n = 2x = 22 chromosomes) is a species with extensive genetic diversity and desirable agronomic traits for coffee breeding programs. However, obtaining a new coffee cultivar through conventional breeding techniques may require more than 30 years of crossing cycles and selection, which hampers the effort of keeping up with market demands and rapidly proposing more resilient to climate change varieties. Although, the application of modern biotechnology tools such as precision genetic engineering technologies may enable a faster cultivar development process. Therefore, we aimed to validate the CRISPR/Cas9 system to generate mutations on a selected genotype of C. canephora, the clone 14. Embryogenic calli and a multiplex binary vector containing two sgRNAs targeting different exons of the CcPDS gene were used. The sgRNAs were under the C. canephora U6 promoter regulation. The target gene encodes phytoene desaturase, an enzyme essential for photosynthesis involved in β-carotene biosynthesis. Somatic seedlings and embryos with albino, variegated and green phenotypes regenerated after Agrobacterium tumefaciens-mediated genetic transformation were analyzed by verifying the insertion of the Cas9 gene and later by sequencing the sgRNAs target regions in the genome of Robusta modified seedlings. Among them, 77% had the expected mutations, and of which, 50% of them had at least one target with a homozygous mutation. The genotype, temperature of co-cultivation with the bacteria, and light intensity used for subsequent embryo regeneration appeared to strongly influence the successful regeneration of plants with a mutated CcPDS gene in the Coffea genus.
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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46
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Kumari D, Prasad BD, Dwivedi P, Hidangmayum A, Sahni S. CRISPR/Cas9 mediated genome editing tools and their possible role in disease resistance mechanism. Mol Biol Rep 2022; 49:11587-11600. [DOI: 10.1007/s11033-022-07851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
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47
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Liu H, Chen W, Li Y, Sun L, Chai Y, Chen H, Nie H, Huang C. CRISPR/Cas9 Technology and Its Utility for Crop Improvement. Int J Mol Sci 2022; 23:10442. [PMID: 36142353 PMCID: PMC9499353 DOI: 10.3390/ijms231810442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid growth of the global population has resulted in a considerable increase in the demand for food crops. However, traditional crop breeding methods will not be able to satisfy the worldwide demand for food in the future. New gene-editing technologies, the most widely used of which is CRISPR/Cas9, may enable the rapid improvement of crop traits. Specifically, CRISPR/Cas9 genome-editing technology involves the use of a guide RNA and a Cas9 protein that can cleave the genome at specific loci. Due to its simplicity and efficiency, the CRISPR/Cas9 system has rapidly become the most widely used tool for editing animal and plant genomes. It is ideal for modifying the traits of many plants, including food crops, and for creating new germplasm materials. In this review, the development of the CRISPR/Cas9 system, the underlying mechanism, and examples of its use for editing genes in important crops are discussed. Furthermore, certain limitations of the CRISPR/Cas9 system and potential solutions are described. This article will provide researchers with important information regarding the use of CRISPR/Cas9 gene-editing technology for crop improvement, plant breeding, and gene functional analyses.
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Affiliation(s)
- Hua Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wendan Chen
- Beijing Key Laboratory of Forest Food Processing and Safety, Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yushu Li
- Beijing Vocational College of Agriculture, Beijing 100097, China
| | - Lei Sun
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yuhong Chai
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haixia Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haochen Nie
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Conglin Huang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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48
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Yang Y, Ke J, Han X, Wuddineh WA, Song GQ, Zhong GY. Removal of a 10-kb Gret1 transposon from VvMybA1 of Vitis vinifera cv. Chardonnay. HORTICULTURE RESEARCH 2022; 9:uhac201. [PMID: 36406285 PMCID: PMC9669667 DOI: 10.1093/hr/uhac201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/31/2022] [Indexed: 06/10/2023]
Abstract
Many white grape cultivars have a nonfunctional VvMybA1 gene due to the presence of a 10-kb Gret1 transposon in its promoter. In this study, we successfully demonstrated removal of the 10-kb Gret1 transposon and functional restoration of a VvMybA1 allele in Vitis vinifera cv. Chardonnay through transgenic expression of Cas9 and two gRNAs simultaneously targeting two junction sequences between Gret1 LTRs and VvMybA1. We generated 67 and 24 Cas9-positive vines via Agrobacterium-mediated and biolistic bombardment transformation, respectively. While the editing efficiencies were as high as 17% for the 5' target site and 65% for the 3' target site, simultaneous editing of both 5' and 3' target sites resulting in the removal of Gret1 transposon from the VvMybA1 promoter was 0.5% or less in most transgenic calli, suggesting that these calli had very limited numbers of cells with the Gret1 removed. Nevertheless, two bombardment-transformed vines, which shared the same unique editing features and were likely derived from a singly edited event, were found to have the Gret1 successfully edited out from one of their two VvMybA1 alleles. The edited allele was functionally restored based on the detection of its expression and a positive coloring assay result in leaves. Precise removal of more than a 10-kb DNA fragment from a gene locus in grape broadens the possibilities of using gene editing technologies to modify various trait genes in grapes and other plants.
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Affiliation(s)
- Yingzhen Yang
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - John Ke
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Xiaoyan Han
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Wegi A Wuddineh
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Guo-qing Song
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
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49
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CRISPR-Based Genome Editing and Its Applications in Woody Plants. Int J Mol Sci 2022; 23:ijms231710175. [PMID: 36077571 PMCID: PMC9456532 DOI: 10.3390/ijms231710175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/31/2022] [Indexed: 12/21/2022] Open
Abstract
CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants.
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50
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Wei X, Pu A, Liu Q, Hou Q, Zhang Y, An X, Long Y, Jiang Y, Dong Z, Wu S, Wan X. The Bibliometric Landscape of Gene Editing Innovation and Regulation in the Worldwide. Cells 2022; 11:cells11172682. [PMID: 36078090 PMCID: PMC9454589 DOI: 10.3390/cells11172682] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Gene editing (GE) has become one of the mainstream bioengineering technologies over the past two decades, mainly fueled by the rapid development of the CRISPR/Cas system since 2012. To date, plenty of articles related to the progress and applications of GE have been published globally, but the objective, quantitative and comprehensive investigations of them are relatively few. Here, 13,980 research articles and reviews published since 1999 were collected by using GE-related queries in the Web of Science. We used bibliometric analysis to investigate the competitiveness and cooperation of leading countries, influential affiliations, and prolific authors. Text clustering methods were used to assess technical trends and research hotspots dynamically. The global application status and regulatory framework were also summarized. This analysis illustrates the bottleneck of the GE innovation and provides insights into the future trajectory of development and application of the technology in various fields, which will be helpful for the popularization of gene editing technology.
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Affiliation(s)
- Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| | - Aqing Pu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Qianqian Liu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yong Zhang
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Zhenying Dong
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
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