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Li W, Chen L, Zhao W, Li Y, Chen Y, Wen T, Liu Z, Huang C, Zhang L, Zhao L. Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit. HORTICULTURE RESEARCH 2024; 11:uhae202. [PMID: 39308791 PMCID: PMC11415240 DOI: 10.1093/hr/uhae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/11/2024] [Indexed: 09/25/2024]
Abstract
Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, tomato fruit color formation is an intricate biological process that remains elusive. In this work we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in the YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme, which may function in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allelic (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were upregulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35 and 47 days post-anthesis compared with the red-fruit tomato cultivar (M82). In vitro and in vivo biochemical analyses indicated that YFT3 (S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that the S126R mutation can impair YFT3 activity. Molecular docking analysis showed that the YFT3 allele has higher ability to recruit isopentenyl pyrophosphate (IPP), but abolishes attachment of the Mg2+ cofactor to IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.
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Affiliation(s)
- Wenzhen Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lulu Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, 2 South Xiwang Avenue, Yancheng 224002, China
| | - Weihua Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yuhang Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ying Chen
- Youlaigu Science and Technology Innovation Center, 588 West Chenfeng, Yushan town, Agriculture Service Center, Kunshan 215300, China
| | - Tengjian Wen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhengjun Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 2708 South Huaxi Avenue, Guiyang 550025, China
| | - Chao Huang
- Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, College of Pharmaceutical Science, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou 310053, China
| | - Lida Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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Liu Y, Xiao W, Liao L, Zheng B, Cao Y, Zhao Y, Zhang RX, Han Y. A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39185667 DOI: 10.1111/jipb.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024]
Abstract
WRKY transcription factors play key roles in plant resistance to various stresses, but their roles in fruit ripening remain largely unknown. Here, we report a WRKY gene PpWRKY14 involved in the regulation of fruit ripening in peach. The expression of PpWRKY14 showed an increasing trend throughout fruit development. PpWRKY14 was a target gene of PpNAC1, a master regulator of peach fruit ripening. PpWRKY14 could directly bind to the promoters of PpACS1 and PpACO1 to induce their expression, and this induction was greatly enhanced when PpWRKY14 formed a dimer with PpNAC1. However, the transcription of PpNAC1 could be directly suppressed by two EIN3/EIL1 genes, PpEIL2 and PpEIL3. The PpEIL2/3 genes were highly expressed at the early stages of fruit development, but their expression was programmed to decrease significantly during the ripening stage, thus derepressing the expression of PpNAC1. These results suggested a PpEIL2/3-PpNAC1-PpWRKY14 module that regulates fruit ripening by modulating ethylene production in peach. Our results provided an insight into the regulatory roles of EIN3/EIL1 and WRKY genes in fruit ripening.
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Affiliation(s)
- Yudi Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Xiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liao Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Beibei Zheng
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yunpeng Cao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yun Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ruo-Xi Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Zhang L, Zhang R, Yan P, Zeng L, Zhao W, Feng H, Mu R, Hou W. PE ( Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant. HORTICULTURE RESEARCH 2024; 11:uhae134. [PMID: 38974191 PMCID: PMC11226868 DOI: 10.1093/hr/uhae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/27/2024] [Indexed: 07/09/2024]
Abstract
Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line 'PI 381159' abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a cleaved amplified polymorphic sequences (CAPS) marker from a distinct SNP located at -735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.
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Affiliation(s)
- Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Runzhi Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ping Yan
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Liqian Zeng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Huiqian Feng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ruyu Mu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
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Akanmu AO, Asemoloye MD, Marchisio MA, Babalola OO. Adoption of CRISPR-Cas for crop production: present status and future prospects. PeerJ 2024; 12:e17402. [PMID: 38860212 PMCID: PMC11164064 DOI: 10.7717/peerj.17402] [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: 06/16/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time. Methods This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security. Results The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops. Conclusion Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.
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Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | - Michael Dare Asemoloye
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
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Yang W, Zhai H, Wu F, Deng L, Chao Y, Meng X, Chen Q, Liu C, Bie X, Sun C, Yu Y, Zhang X, Zhang X, Chang Z, Xue M, Zhao Y, Meng X, Li B, Zhang X, Zhang D, Zhao X, Gao C, Li J, Li C. Peptide REF1 is a local wound signal promoting plant regeneration. Cell 2024; 187:3024-3038.e14. [PMID: 38781969 DOI: 10.1016/j.cell.2024.04.040] [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: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Plants frequently encounter wounding and have evolved an extraordinary regenerative capacity to heal the wounds. However, the wound signal that triggers regenerative responses has not been identified. Here, through characterization of a tomato mutant defective in both wound-induced defense and regeneration, we demonstrate that in tomato, a plant elicitor peptide (Pep), REGENERATION FACTOR1 (REF1), acts as a systemin-independent local wound signal that primarily regulates local defense responses and regenerative responses in response to wounding. We further identified PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE1 (PORK1) as the receptor perceiving REF1 signal for plant regeneration. REF1-PORK1-mediated signaling promotes regeneration via activating WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), a master regulator of wound-induced cellular reprogramming in plants. Thus, REF1-PORK1 signaling represents a conserved phytocytokine pathway to initiate, amplify, and stabilize a signaling cascade that orchestrates wound-triggered organ regeneration. Application of REF1 provides a simple method to boost the regeneration and transformation efficiency of recalcitrant crops.
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Affiliation(s)
- Wentao Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Huawei Zhai
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Fangming Wu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Yu Chao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianwen Meng
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qian Chen
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Chenhuan Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Chuanlong Sun
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yang Yu
- Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiaofei Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyue Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeqian Chang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Xue
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yajie Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiangbing Meng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Boshu Li
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiansheng Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Dajian Zhang
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiangyu Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Caixia Gao
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuanyou Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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Su T, Zhang XF, Wu GZ. Functional conservation of GENOMES UNCOUPLED1 in plastid-to-nucleus retrograde signaling in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112053. [PMID: 38417718 DOI: 10.1016/j.plantsci.2024.112053] [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: 10/19/2023] [Revised: 01/20/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Retrograde signaling between plastids and the nucleus is vital for chloroplast biogenesis and environmental responses. GENOMES UNCOUPLED1 (GUN1) was proposed to be a central integrator of multiple retrograde signaling pathways in the model plant Arabidopsis thaliana (Arabidopsis). However, the function of GUN1 orthologs in other plant species has not been well studied. Here, we found that many GUN1 orthologs from the Solanaceae family have a short N-terminus before the first pentatricopeptide repeat (PPR) motif which is predicted as intrinsically disordered regions (IDRs). Functional analyses of tomato (Solanum lycopersicum L.) GUN1 (SlGUN1), which does not contain N-terminal IDRs, show that it can complement the GUN phenotype of the Arabidopsis gun1 mutant (Atgun1). However, in contrast to the AtGUN1 protein, which does contain the N-terminal IDRs, the SlGUN1 protein is highly accumulated even after chloroplast biogenesis is completed, suggesting that the N-terminal IDRs may determine the stability of the GUN1 protein. Furthermore, we generated tomato Slgun1 genome-edited mutants via the CRISPR-Cas9 system. The Slgun1 mutants exhibited a typical GUN phenotype under lincomycin (Lin) or norflurazon (NF) treatment. Moreover, Slgun1 mutants are hypersensitive to low concentrations of Lin or NF. Taken together, our results suggest that, although lacking the N-terminal IDRs, SlGUN1 plays conserved roles in plastid retrograde signaling in tomato plants.
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Affiliation(s)
- Tong Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Xiao-Fan Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
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7
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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8
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Yang T, Deng L, Wang Q, Sun C, Ali M, Wu F, Zhai H, Xu Q, Xin P, Cheng S, Chu J, Huang T, Li CB, Li C. Tomato CYP94C1 inactivates bioactive JA-Ile to attenuate jasmonate-mediated defense during fruit ripening. MOLECULAR PLANT 2024; 17:509-512. [PMID: 38327053 DOI: 10.1016/j.molp.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/16/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
As the master regulators of the ET signaling pathway, EIL transcription factors directly activate the expression of CYP94C1 to inactivate bioactive JA-Ile, thereby attenuating JA-mediated defense during fruit ripening. Knockout of CYP94C1 improves tomato fruit resistance to necrotrophs without compromising fruit quality.
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Affiliation(s)
- Tianxia Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Deng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Taishan Academy of Tomato Innovation, Tai'an 271018, China.
| | - Qinyang Wang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanlong Sun
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Taishan Academy of Tomato Innovation, Tai'an 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Muhammad Ali
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangming Wu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhai
- Taishan Academy of Tomato Innovation, Tai'an 271018, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Qian Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Peiyong Xin
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shujing Cheng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Huang
- Institute of Vegetable, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Chang-Bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chuanyou Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Taishan Academy of Tomato Innovation, Tai'an 271018, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Liu J, Zhang C, Sun H, Zang Y, Meng X, Zhai H, Chen Q, Li C. A natural variation in SlSCaBP8 promoter contributes to the loss of saline-alkaline tolerance during tomato improvement. HORTICULTURE RESEARCH 2024; 11:uhae055. [PMID: 38659442 PMCID: PMC11040208 DOI: 10.1093/hr/uhae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
Saline-alkaline stress is a worldwide problem that threatens the growth and yield of crops. However, how crops adapt to saline-alkaline stress remains less studied. Here we show that saline-alkaline tolerance was compromised during tomato domestication and improvement, and a natural variation in the promoter of SlSCaBP8, an EF-hand Ca2+ binding protein, contributed to the loss of saline-alkaline tolerance during tomato improvement. The biochemical and genetic data showed that SlSCaBP8 is a positive regulator of saline-alkaline tolerance in tomato. The introgression line Pi-75, derived from a cross between wild Solanum pimpinellifolium LA1589 and cultivar E6203, containing the SlSCaBP8LA1589 locus, showed stronger saline-alkaline tolerance than E6203. Pi-75 and LA1589 also showed enhanced saline-alkaline-induced SlSCaBP8 expression than that of E6203. By sequence analysis, a natural variation was found in the promoter of SlSCaBP8 and the accessions with the wild haplotype showed enhanced saline-alkaline tolerance compared with the cultivar haplotype. Our studies clarify the mechanism of saline-alkaline tolerance conferred by SlSCaBP8 and provide an important natural variation in the promoter of SlSCaBP8 for tomato breeding.
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Affiliation(s)
- Jian Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chi Zhang
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Heyao Sun
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yinqiang Zang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xianwen Meng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Huawei Zhai
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Qian Chen
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Chuanyou Li
- College of Life Science, Shandong Agricultural University, Tai’an, Shandong 271018, China
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10
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Larriba E, Yaroshko O, Pérez-Pérez JM. Recent Advances in Tomato Gene Editing. Int J Mol Sci 2024; 25:2606. [PMID: 38473859 DOI: 10.3390/ijms25052606] [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: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.
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Affiliation(s)
- Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Olha Yaroshko
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
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11
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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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12
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Baranov D, Timerbaev V. Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches. Int J Mol Sci 2024; 25:760. [PMID: 38255834 PMCID: PMC10815249 DOI: 10.3390/ijms25020760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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13
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Zhang RX, Liu Y, Zhang X, Chen X, Sun J, Zhao Y, Zhang J, Yao JL, Liao L, Zhou H, Han Y. Two adjacent NAC transcription factors regulate fruit maturity date and flavor in peach. THE NEW PHYTOLOGIST 2024; 241:632-649. [PMID: 37933224 DOI: 10.1111/nph.19372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023]
Abstract
Although maturity date (MD) is an essential factor affecting fresh fruit marketing and has a pleiotropic effect on fruit taste qualities, the underlying mechanisms remain largely unclear. In this study, we functionally characterized two adjacent NAM-ATAF1/2-CUC2 (NAC) transcription factors (TFs), PpNAC1 and PpNAC5, both of which were associated with fruit MD in peach. PpNAC1 and PpNAC5 were found capable of activating transcription of genes associated with cell elongation, cell wall degradation and ethylene biosynthesis, suggesting their regulatory roles in fruit enlargement and ripening. Furthermore, PpNAC1 and PpNAC5 had pleiotropic effects on fruit taste due to their ability to activate transcription of genes for sugar accumulation and organic acid degradation. Interestingly, both PpNAC1 and PpNAC5 orthologues were found in fruit-producing angiosperms and adjacently arranged in all 91 tested dicots but absent in fruitless gymnosperms, suggesting their important roles in fruit development. Our results provide insight into the regulatory roles of NAC TFs in MD and fruit taste.
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Affiliation(s)
- Ruo-Xi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yudi Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xian Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Juanli Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Yun Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jinyun Zhang
- Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Hui Zhou
- Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province), Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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14
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Hu G, Zhang D, Luo D, Sun W, Zhou R, Hong Z, Munir S, Ye Z, Yang C, Zhang J, Wang T. SlTCP24 and SlTCP29 synergistically regulate compound leaf development through interacting with SlAS2 and activating transcription of SlCKX2 in tomato. THE NEW PHYTOLOGIST 2023; 240:1275-1291. [PMID: 37615215 DOI: 10.1111/nph.19221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
The complexity of compound leaves results primarily from the leaflet initiation and arrangement during leaf development. However, the molecular mechanism underlying compound leaf development remains a central research question. SlTCP24 and SlTCP29, two plant-specific transcription factors with the conserved TCP motif, are shown here to synergistically regulate compound leaf development in tomato. When both of them were knocked out simultaneously, the number of leaflets significantly increased, and the shape of the leaves became more complex. SlTCP24 and SlTCP29 could form both homodimers and heterodimers, and such dimerization was impeded by the leaf polarity regulator SlAS2, which interacted with SlTCP24 and SlTCP29. SlTCP24 and SlTCP29 could bind to the TCP-binding cis-element of the SlCKX2 promoter and activate its transcription. Transgenic plants with SlTCP24 and SlTCP29 double-gene knockout had a lowered transcript level of SlCKX2 and an elevated level of cytokinin. This work led to the identification of two key regulators of tomato compound leaf development and their targeted genes involved in cytokinin metabolic pathway. A model of regulation of compound leaf development was proposed based on observations of this study.
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Affiliation(s)
- Guoyu Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Danqiu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Dan Luo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Wenhui Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Rijin Zhou
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Shoaib Munir
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Changxian Yang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
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15
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Zhu Q, Deng L, Chen J, Rodríguez GR, Sun C, Chang Z, Yang T, Zhai H, Jiang H, Topcu Y, Francis D, Hutton S, Sun L, Li CB, van der Knaap E, Li C. Redesigning the tomato fruit shape for mechanized production. NATURE PLANTS 2023; 9:1659-1674. [PMID: 37723204 DOI: 10.1038/s41477-023-01522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023]
Abstract
Crop breeding for mechanized harvesting has driven modern agriculture. In tomato, machine harvesting for industrial processing varieties became the norm in the 1970s. However, fresh-market varieties whose fruits are suitable for mechanical harvesting are difficult to breed because of associated reduction in flavour and nutritional qualities. Here we report the cloning and functional characterization of fs8.1, which controls the elongated fruit shape and crush resistance of machine-harvestable processing tomatoes. FS8.1 encodes a non-canonical GT-2 factor that activates the expression of cell-cycle inhibitor genes through the formation of a transcriptional module with the canonical GT-2 factor SlGT-16. The fs8.1 mutation results in a lower inhibitory effect on the cell proliferation of the ovary wall, leading to elongated fruits with enhanced compression resistance. Our study provides a potential route for introducing the beneficial allele into fresh-market tomatoes without reducing quality, thereby facilitating mechanical harvesting.
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Affiliation(s)
- Qiang Zhu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Jie Chen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Gustavo R Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Rosario, Argentina
| | - Chuanlong Sun
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Zeqian Chang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Tianxia Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Huawei Zhai
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Hongling Jiang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yasin Topcu
- Institute of Plant Breeding, Department of Horticulture, University of Georgia, Athens, GA, USA
- Batı Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - David Francis
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, USA
| | - Samuel Hutton
- Gulf Coast Research and Education Center, University of Florida, Gainesville, FL, USA
| | - Liang Sun
- College of Horticulture, China Agricultural University, Beijing, China
| | - Chang-Bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Esther van der Knaap
- Institute of Plant Breeding, Department of Horticulture, University of Georgia, Athens, GA, USA
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.
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16
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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17
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Bashir T, Ul Haq SA, Masoom S, Ibdah M, Husaini AM. Quality trait improvement in horticultural crops: OMICS and modern biotechnological approaches. Mol Biol Rep 2023; 50:8729-8742. [PMID: 37642759 DOI: 10.1007/s11033-023-08728-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
Horticultural crops are an essential part of food and nutritional security. Moreover, these form an integral part of the agricultural economy and have enormous economic potential. They are a rich source of nutrients that are beneficial to human health. Plant breeding of horticultural crops has focussed primarily on increasing the productivity and related traits of these crops. However, fruit and vegetable quality is paramount to their perishability, marketability, and consumer acceptance. The improved nutritional value is beneficial to underprivileged and undernourished communities. Due to a declining genetic base, conventional plant breeding does not contribute much to quality improvement as the existing natural allelic variations and crossing barriers between cultivated and wild species limit it. Over the past two decades, 'omics' and modern biotechnological approaches have made it possible to decode the complex genomes of crop plants, assign functions to the otherwise many unknown genes, and develop genome-wide DNA markers. Genetic engineering has enabled the validation of these genes and the introduction of crucial agronomic traits influencing various quality parameters directly or indirectly. This review discusses the significant advances in the quality improvement of horticultural crops, including shelf life, aroma, browning, nutritional value, colour, and many other related traits.
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Affiliation(s)
- Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Salsabeel Masoom
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Mwafaq Ibdah
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay, 30095, Israel
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India.
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18
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Zhou M, Deng L, Yuan G, Zhao W, Ma M, Sun C, Du M, Li C, Li C. Rapid generation of a tomato male sterility system and its feasible application in hybrid seed production. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:197. [PMID: 37608233 DOI: 10.1007/s00122-023-04428-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/24/2023] [Indexed: 08/24/2023]
Abstract
KEY MESSAGE A practical approach for the rapid generation and feasible application of green hypocotyl male-sterile (GHMS) tm6 dfr lines in tomato hybrid breeding was established. Male sterility enables reduced cost and high seed purity during hybrid seed production. However, progress toward its commercial application has been slow in tomato due to the disadvantages of most natural male-sterile mutants. Here, we developed a practical method for efficient tomato hybrid seed production using a male-sterile system with visible marker, which was rapidly generated by CRISPR/Cas9-mediated gene editing. Two closely linked genes, TM6 and DFR, which were reported to be candidates of ms15 (male sterile-15) and aw (anthocyanin without) locus, respectively, were knocked out simultaneously in two elite tomato inbred lines. Mutagenesis of both genes generated green hypocotyl male-sterile (GHMS) lines. The GHMS lines exhibited male sterility across different genetic backgrounds and environmental conditions. They also showed green hypocotyl due to defective anthocyanin accumulation, which serves as a reliable visible marker for selecting male-sterile plants at the seedling stage. We further proposed a strategy for multiplying the GHMS system and verified its high efficiency in stable male sterility propagation. Moreover, elite hybrid seeds were produced using GHMS system for potential side effects evaluation, and no adverse influences were found on seed yield, seed quality as well as important agronomic traits. This study provides a practical approach for the rapid generation and feasible application of male sterility in tomato hybrid breeding.
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Affiliation(s)
- Ming Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guoliang Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wei Zhao
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingyang Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chuanlong Sun
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Minmin Du
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Changbao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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19
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Naeem M, Zhao W, Ahmad N, Zhao L. Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation. Funct Integr Genomics 2023; 23:243. [PMID: 37453947 DOI: 10.1007/s10142-023-01162-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Fruit color is a genetic trait and a key factor for consumer acceptability and is therefore receiving increasing importance in several breeding programs. Plant pigments offer plants with a variety of colored organs that attract animals for pollination, favoring seed dispersers and conservation of species. The pigments inside plant cells not only play a light-harvesting role but also provide protection against light damage and exhibit nutritional and ecological value for health and visual pleasure in humans. Tomato (Solanum lycopersicum) is a leading vegetable crop; its fruit color formation is associated with the accumulation of several natural pigments, which include carotenoids in the pericarp, flavonoids in the peel, as well as the breakdown of chlorophyll during fruit ripening. To improve tomato fruit quality, several techniques, such as genetic engineering and genome editing, have been used to alter fruit color and regulate the accumulation of secondary metabolites in related pathways. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-based systems have been extensively used for genome editing in many crops, including tomatoes, and promising results have been achieved using modified CRISPR systems, including CAS9 (CRISPR/CRISPR-associated-protein) and CRISPR/Cas12a systems. These advanced tools in biotechnology and whole genome sequencing of various tomato species will certainly advance the breeding of tomato fruit color with a high degree of precision. Here, we attempt to summarize the current advancement and effective application of genetic engineering techniques that provide further flexibility for fruit color formation. Furthermore, we have also discussed the challenges and opportunities of genetic engineering and genome editing to improve tomato fruit color.
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Affiliation(s)
- Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Weihua Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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20
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Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
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Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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21
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Wang X, Liu Z, Bai J, Sun S, Song J, Li R, Cui X. Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching. THE PLANT CELL 2023; 35:2062-2078. [PMID: 36881857 PMCID: PMC10226558 DOI: 10.1093/plcell/koad065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/30/2023]
Abstract
Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.
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Affiliation(s)
- Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
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22
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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23
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Rosa-Martínez E, Bovy A, Plazas M, Tikunov Y, Prohens J, Pereira-Dias L. Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits. FRONTIERS IN PLANT SCIENCE 2023; 14:1135237. [PMID: 37025131 PMCID: PMC10070870 DOI: 10.3389/fpls.2023.1135237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.
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Affiliation(s)
- Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Arnaud Bovy
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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24
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Dong R, Yuan Y, Liu Z, Sun S, Wang H, Ren H, Cui X, Li R. ASYMMETRIC LEAVES 2 and ASYMMETRIC LEAVES 2-LIKE are partially redundant genes and essential for fruit development in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36932869 DOI: 10.1111/tpj.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 03/09/2023] [Indexed: 06/08/2023]
Abstract
Fruit size and shape are controlled by genes expressed during the early developmental stages of fruit. Although the function of ASYMMETRIC LEAVES 2 (AS2) in promoting leaf adaxial cell fates has been well characterized in Arabidopsis thaliana, the molecular mechanisms conferring freshy fruit development as a spatial-temporal expression gene in tomato pericarp remain unclear. In the present study, we verified the transcription of SlAS2 and SlAS2L, two homologs of AS2, in the pericarp during early fruit development. Disruption of SlAS2 or SlAS2L caused a significant decrease in pericarp thickness as a result of a reduction in the number of pericarp cell layers and cell area, leading to smaller tomato fruit size, which revealed their critical roles in tomato fruit development. In addition, leaves and stamens exhibited severe morphological defects in slas2 and slas2l single mutants, as well as in the double mutants. These results demonstrated the redundant and pleiotropic functions of SlAS2 and SlAS2L in tomato fruit development. Yeast two-hybrid and split-luciferase complementation assays showed that both SlAS2 and SlAS2L physically interact with SlAS1. Molecular analyses further indicated that SlAS2 and SlAS2L regulate various downstream genes in leaf and fruit development, and that some genes participating in the regulation of cell division and cell differentiation in the tomato pericarp are affected by these genes. Our findings demonstrate that SlAS2 and SlAS2L are vital transcription factors required for tomato fruit development.
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Affiliation(s)
- Rongrong Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yaqin Yuan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haijing Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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25
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Deng L, Yang T, Li Q, Chang Z, Sun C, Jiang H, Meng X, Huang T, Li CB, Zhong S, Li C. Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors. THE PLANT CELL 2023; 35:1038-1057. [PMID: 36471914 PMCID: PMC10015170 DOI: 10.1093/plcell/koac349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Fruit ripening relies on the precise spatiotemporal control of RNA polymerase II (Pol II)-dependent gene transcription, and the evolutionarily conserved Mediator (MED) coactivator complex plays an essential role in this process. In tomato (Solanum lycopersicum), a model climacteric fruit, ripening is tightly coordinated by ethylene and several key transcription factors. However, the mechanism underlying the transmission of context-specific regulatory signals from these ripening-related transcription factors to the Pol II transcription machinery remains unknown. Here, we report the mechanistic function of MED25, a subunit of the plant Mediator transcriptional coactivator complex, in controlling the ethylene-mediated transcriptional program during fruit ripening. Multiple lines of evidence indicate that MED25 physically interacts with the master transcription factors of the ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) family, thereby playing an essential role in pre-initiation complex formation during ethylene-induced gene transcription. We also show that MED25 forms a transcriptional module with EIL1 to regulate the expression of ripening-related regulatory as well as structural genes through promoter binding. Furthermore, the EIL1-MED25 module orchestrates both positive and negative feedback transcriptional circuits, along with its downstream regulators, to fine-tune ethylene homeostasis during fruit ripening.
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Affiliation(s)
- Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianxia Yang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Li
- Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zeqian Chang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanlong Sun
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongling Jiang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianwen Meng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Tingting Huang
- Institute of Vegetable, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Chang-Bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong 999077, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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26
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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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27
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Tiwari JK, Singh AK, Behera TK. CRISPR/Cas genome editing in tomato improvement: Advances and applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1121209. [PMID: 36909403 PMCID: PMC9995852 DOI: 10.3389/fpls.2023.1121209] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 06/12/2023]
Abstract
The narrow genetic base of tomato poses serious challenges in breeding. Hence, with the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, fast and efficient breeding has become possible in tomato breeding. Many traits have been edited and functionally characterized using CRISPR/Cas9 in tomato such as plant architecture and flower characters (e.g. leaf, stem, flower, male sterility, fruit, parthenocarpy), fruit ripening, quality and nutrition (e.g., lycopene, carotenoid, GABA, TSS, anthocyanin, shelf-life), disease resistance (e.g. TYLCV, powdery mildew, late blight), abiotic stress tolerance (e.g. heat, drought, salinity), C-N metabolism, and herbicide resistance. CRISPR/Cas9 has been proven in introgression of de novo domestication of elite traits from wild relatives to the cultivated tomato and vice versa. Innovations in CRISPR/Cas allow the use of online tools for single guide RNA design and multiplexing, cloning (e.g. Golden Gate cloning, GoldenBraid, and BioBrick technology), robust CRISPR/Cas constructs, efficient transformation protocols such as Agrobacterium, and DNA-free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex, Cas9 variants like PAM-free Cas12a, and Cas9-NG/XNG-Cas9, homologous recombination (HR)-based gene knock-in (HKI) by geminivirus replicon, and base/prime editing (Target-AID technology). This mini-review highlights the current research advances in CRISPR/Cas for fast and efficient breeding of tomato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anand Kumar Singh
- Division of Horticulture, Indian Council of Agricultural Research, Krishi Anusandhan Bhawan - II, Pusa, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Das T, Anand U, Pal T, Mandal S, Kumar M, Radha, Gopalakrishnan AV, Lastra JMPDL, Dey A. Exploring the potential of CRISPR/Cas genome editing for vegetable crop improvement: An overview of challenges and approaches. Biotechnol Bioeng 2023; 120:1215-1228. [PMID: 36740587 DOI: 10.1002/bit.28344] [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: 06/02/2022] [Revised: 12/12/2022] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Vegetables provide many nutrients in the form of fiber, vitamins, and minerals, which make them an important part of our diet. Numerous biotic and abiotic stresses can affect crop growth, quality, and yield. Traditional and modern breeding strategies to improve plant traits are slow and resource intensive. Therefore, it is necessary to find new approaches for crop improvement. Clustered regularly interspaced short palindromic repeats/CRISPR associated 9 (CRISPR/Cas9) is a genome editing tool that can be used to modify targeted genes for desirable traits with greater efficiency and accuracy. By using CRISPR/Cas9 editing to precisely mutate key genes, it is possible to rapidly generate new germplasm resources for the promotion of important agronomic traits. This is made possible by the availability of whole genome sequencing data and information on the function of genes responsible for important traits. In addition, CRISPR/Cas9 systems have revolutionized agriculture, making genome editing more versatile. Currently, genome editing of vegetable crops is limited to a few vegetable varieties (tomato, sweet potato, potato, carrot, squash, eggplant, etc.) due to lack of regeneration protocols and sufficient genome sequencing data. In this article, we summarize recent studies on the application of CRISPR/Cas9 in improving vegetable trait development and the potential for future improvement.
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Affiliation(s)
- Tuyelee Das
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Tarun Pal
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, Tenerife, Spain
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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Wang M, Wang H, Li K, Li X, Wang X, Wang Z. Review of CRISPR/Cas Systems on Detection of Nucleotide Sequences. Foods 2023; 12:foods12030477. [PMID: 36766007 PMCID: PMC9913930 DOI: 10.3390/foods12030477] [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: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Nowadays, with the rapid development of biotechnology, the CRISPR/Cas technology in particular has produced many new traits and products. Therefore, rapid and high-resolution detection methods for biotechnology products are urgently needed, which is extremely important for safety regulation. Recently, in addition to being gene editing tools, CRISPR/Cas systems have also been used in detection of various targets. CRISPR/Cas systems can be successfully used to detect nucleic acids, proteins, metal ions and others in combination with a variety of technologies, with great application prospects in the future. However, there are still some challenges need to be addressed. In this review, we will list some detection methods of genetically modified (GM) crops, gene-edited crops and single-nucleotide polymorphisms (SNPs) based on CRISPR/Cas systems, hoping to bring some inspiration or ideas to readers.
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Affiliation(s)
- Mengyu Wang
- Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Ministry of Agriculture and Rural Affairs, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haoqian Wang
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China
| | - Kai Li
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoman Li
- Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Ministry of Agriculture and Rural Affairs, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xujing Wang
- Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Ministry of Agriculture and Rural Affairs, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhixing Wang
- Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Ministry of Agriculture and Rural Affairs, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence:
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Devi R, Chauhan S, Dhillon TS. Genome editing for vegetable crop improvement: Challenges and future prospects. Front Genet 2022; 13:1037091. [PMID: 36482900 PMCID: PMC9723405 DOI: 10.3389/fgene.2022.1037091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/28/2022] [Indexed: 09/10/2024] Open
Abstract
Vegetable crops are known as protective foods due to their potential role in a balanced human diet, especially for vegetarians as they are a rich source of vitamins and minerals along with dietary fibers. Many biotic and abiotic stresses threaten the crop growth, yield and quality of these crops. These crops are annual, biennial and perennial in breeding behavior. Traditional breeding strategies pose many challenges in improving economic crop traits. As in most of the cases the large number of backcrosses and stringent selection pressure is required for the introgression of the useful traits into the germplasm, which is time and labour-intensive process. Plant scientists have improved economic traits like yield, quality, biotic stress resistance, abiotic stress tolerance, and improved nutritional quality of crops more precisely and accurately through the use of the revolutionary breeding method known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9). The high mutation efficiency, less off-target consequences and simplicity of this technique has made it possible to attain novel germplasm resources through gene-directed mutation. It facilitates mutagenic response even in complicated genomes which are difficult to breed using traditional approaches. The revelation of functions of important genes with the advancement of whole-genome sequencing has facilitated the CRISPR-Cas9 editing to mutate the desired target genes. This technology speeds up the creation of new germplasm resources having better agro-economical traits. This review entails a detailed description of CRISPR-Cas9 gene editing technology along with its potential applications in olericulture, challenges faced and future prospects.
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Affiliation(s)
- Ruma Devi
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
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Yang T, Ali M, Lin L, Li P, He H, Zhu Q, Sun C, Wu N, Zhang X, Huang T, Li CB, Li C, Deng L. Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing. HORTICULTURE RESEARCH 2022; 10:uhac214. [PMID: 36643741 PMCID: PMC9832834 DOI: 10.1093/hr/uhac214] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/14/2022] [Indexed: 05/24/2023]
Abstract
Fruit color is an important horticultural trait, which greatly affects consumer preferences. In tomato, fruit color is determined by the accumulation of different pigments, such as carotenoids in the pericarp and flavonoids in the peel, along with the degradation of chlorophyll during fruit ripening. Since fruit color is a multigenic trait, it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding, and the avoidance of linkage drag during this process is difficult. Here, we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes (PSY1, MYB12, and SGR1). Using this strategy, the red-fruited cultivar 'Ailsa Craig' has been engineered to a series of tomato genotypes with different fruit colors, including yellow, brown, pink, light-yellow, pink-brown, yellow-green, and light green. Compared with traditional crossbreeding, this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1 year. Most importantly, it does not alter other important agronomic traits, like yield and fruit quality. Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.
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Affiliation(s)
| | | | | | - Ping Li
- Institute of Vegetable, Qingdao Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Hongju He
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qiang Zhu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanlong Sun
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofei Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Huang
- Institute of Vegetable, Qingdao Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Chang-Bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | | | - Lei Deng
- Corresponding authors. E-mail: ;
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Gu M, Lu Q, Liu Y, Cui M, Si Y, Wu H, Chai T, Ling HQ. Requirement and functional redundancy of two large ribonucleotide reductase subunit genes for cell cycle, chloroplast biogenesis and photosynthesis in tomato. ANNALS OF BOTANY 2022; 130:173-187. [PMID: 35700127 PMCID: PMC9445600 DOI: 10.1093/aob/mcac078] [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: 02/23/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Ribonucleotide reductase (RNR), functioning in the de novo synthesis of deoxyribonucleoside triphosphates (dNTPs), is crucial for DNA replication and cell cycle progression. In most plants, the large subunits of RNR have more than one homologous gene. However, the different functions of these homologous genes in plant development remain unknown. In this study, we obtained the mutants of two large subunits of RNR in tomato and studied their functions. METHODS The mutant ylc1 was obtained by ethyl methyl sulfonate (EMS) treatment. Through map-based cloning, complementation and knock-out experiments, it was confirmed that YLC1 encodes a large subunit of RNR (SlRNRL1). The expression level of the genes related to cell cycle progression, chloroplast biogenesis and photosynthesis was assessed by RNA-sequencing. In addition, we knocked out SlRNRL2 (a SlRNRL1 homologue) using CRISPR-Cas9 technology in the tomato genome, and we down-regulated SlRNRL2 expression in the genetic background of slrnrl1-1 using a tobacco rattle virus-induced gene silencing (VIGS) system. KEY RESULTS The mutant slrnrl1 exhibited dwarf stature, chlorotic young leaves and smaller fruits. Physiological and transcriptomic analyses indicated that SlRNRL1 plays a crucial role in the regulation of cell cycle progression, chloroplast biogenesis and photosynthesis in tomato. The slrnrl2 mutant did not exhibit any visible phenotype. SlRNRL2 has a redundant function with SlRNRL1, and the double mutant slrnrl1slrnrl2 is lethal. CONCLUSIONS SlRNRL1 is essential for cell cycle progression, chloroplast biogenesis and photosynthesis. In addition, SlRNRL1 and SlRNRL2 possess redundant functions and at least one of these RNRLs is required for tomato survival, growth and development.
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Affiliation(s)
| | | | - Yi Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Man Cui
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yaoqi Si
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Tuanyao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Ming M, Long H, Ye Z, Pan C, Chen J, Tian R, Sun C, Xue Y, Zhang Y, Li J, Qi Y, Wu J. Highly efficient CRISPR systems for loss-of-function and gain-of-function research in pear calli. HORTICULTURE RESEARCH 2022; 9:uhac148. [PMID: 36072833 PMCID: PMC9437716 DOI: 10.1093/hr/uhac148] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
CRISPR/Cas systems have been widely used for genome engineering in many plant species. However, their potentials have remained largely untapped in fruit crops, particularly in pear, due to the high levels of genomic heterozygosity and difficulties in tissue culture and stable transformation. To date, only a few reports on the application of the CRISPR/Cas9 system in pear have been documented, and have shown very low editing efficiency. Here we report a highly efficient CRISPR toolbox for loss-of-function and gain-of-function research in pear. We compared four different CRISPR/Cas9 expression systems for loss-of-function analysis and identified a potent system that showed nearly 100% editing efficiency for multi-site mutagenesis. To expand the targeting scope, we further tested different CRISPR/Cas12a and Cas12b systems in pear for the first time, albeit with low editing efficiency. In addition, we established a CRISPR activation (CRISPRa) system for multiplexed gene activation in pear calli for gain-of-function analysis. Furthermore, we successfully engineered the anthocyanin and lignin biosynthesis pathways using both CRISPR/Cas9 and CRISPRa systems in pear calli. Taking these results together, we have built a highly efficient CRISPR toolbox for genome editing and gene regulation, paving the way for functional genomics studies as well as molecular breeding in pear.
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Affiliation(s)
- Meiling Ming
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjun Long
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhicheng Ye
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Jiali Chen
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Rong Tian
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Congrui Sun
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongsong Xue
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Jun Wu
- Corresponding authors. E-mail: ,
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Yuan Y, Ren S, Liu X, Su L, Wu Y, Zhang W, Li Y, Jiang Y, Wang H, Fu R, Bouzayen M, Liu M, Zhang Y. SlWRKY35 positively regulates carotenoid biosynthesis by activating the MEP pathway in tomato fruit. THE NEW PHYTOLOGIST 2022; 234:164-178. [PMID: 35048386 DOI: 10.1111/nph.17977] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Carotenoids are vital phytonutrients widely recognised for their health benefits. Therefore, it is vital to thoroughly investigate the metabolic regulatory network underlying carotenoid biosynthesis and accumulation to open new leads towards improving their contents in vegetables and crops. The outcome of our study defines SlWRKY35 as a positive regulator of carotenoid biosynthesis in tomato. SlWRKY35 can directly activate the expression of the 1-deoxy-d-xylulose 5-phosphate synthase (SlDXS1) gene to reprogramme metabolism towards the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, leading to enhanced carotenoid accumulation. We also show that the master regulator SlRIN directly regulates the expression of SlWRKY35 during tomato fruit ripening. Compared with the SlLCYE overexpression lines, coexpression of SlWRKY35 and SlLCYE can further enhance lutein production in transgenic tomato fruit, indicating that SlWRKY35 represents a potential target towards designing innovative metabolic engineering strategies for carotenoid derivatives. In addition to providing new insights into the metabolic regulatory network associated with tomato fruit ripening, our data define a new tool for improving fruit content in specific carotenoid compounds.
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Affiliation(s)
- Yong Yuan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Siyan Ren
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xiaofeng Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Liyang Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yu Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wen Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Li
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Yidan Jiang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hsihua Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mondher Bouzayen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- GBF, University of Toulouse, INRA, Castanet-Tolosan, 31320, France
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Nagamine A, Ezura H. Genome Editing for Improving Crop Nutrition. Front Genome Ed 2022; 4:850104. [PMID: 35224538 PMCID: PMC8864126 DOI: 10.3389/fgeed.2022.850104] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genome editing technologies, including CRISPR/Cas9 and TALEN, are excellent genetic modification techniques and are being proven to be powerful tools not only in the field of basic science but also in the field of crop breeding. Recently, two genome-edited crops targeted for nutritional improvement, high GABA tomatoes and high oleic acid soybeans, have been released to the market. Nutritional improvement in cultivated crops has been a major target of conventional genetic modification technologies as well as classical breeding methods. Mutations created by genome editing are considered to be almost identical to spontaneous genetic mutations because the mutation inducer, the transformed foreign gene, can be completely eliminated from the final genome-edited hosts after causing the mutation. Therefore, genome-edited crops are expected to be relatively easy to supply to the market, unlike GMO crops. On the other hand, due to their technical feature, the main goal of current genome-edited crop creation is often the total or partial disruption of genes rather than gene delivery. Therefore, to obtain the desired trait using genome editing technology, in some cases, a different approach from that of genetic recombination technology may be required. In this mini-review, we will review several nutritional traits in crops that have been considered suitable targets for genome editing, including the two examples mentioned above, and discuss how genome editing technology can be an effective breeding technology for improving nutritional traits in crops.
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Affiliation(s)
- Ai Nagamine
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Hiroshi Ezura,
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Yang Y, Xu C, Shen Z, Yan C. Crop Quality Improvement Through Genome Editing Strategy. Front Genome Ed 2022; 3:819687. [PMID: 35174353 PMCID: PMC8841430 DOI: 10.3389/fgeed.2021.819687] [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: 11/22/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Good quality of crops has always been the most concerning aspect for breeders and consumers. However, crop quality is a complex trait affected by both the genetic systems and environmental factors, thus, it is difficult to improve through traditional breeding strategies. Recently, the CRISPR/Cas9 genome editing system, enabling efficiently targeted modification, has revolutionized the field of quality improvement in most crops. In this review, we briefly review the various genome editing ability of the CRISPR/Cas9 system, such as gene knockout, knock-in or replacement, base editing, prime editing, and gene expression regulation. In addition, we highlight the advances in crop quality improvement applying the CRISPR/Cas9 system in four main aspects: macronutrients, micronutrients, anti-nutritional factors and others. Finally, the potential challenges and future perspectives of genome editing in crop quality improvement is also discussed.
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Affiliation(s)
- Yihao Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Chenda Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Ziyan Shen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Changjie Yan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
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Zhou M, Deng L, Guo S, Yuan G, Li C, Li C. Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way. HORTICULTURE RESEARCH 2022; 9:6498066. [PMID: 35031800 PMCID: PMC8788357 DOI: 10.1093/hr/uhab045] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 05/31/2023]
Abstract
Carotenoid pigments confer photoprotection and visual attraction and serve as precursors for many important signaling molecules. Herein, the orange-fruited phenotype of a tomato elite inbred line resulting from sharply reduced carotenoid levels and an increased β-carotene-to-lycopene ratio in fruit was shown to be controlled by a single recessive gene, oft3. BSA-Seq combined with fine mapping delimited the oft3 gene to a 71.23 kb interval on chromosome 4, including eight genes. Finally, the oft3 candidate gene SlIDI1, harboring a 116 bp deletion mutation, was identified by genome sequence analysis. Further functional complementation and CRISPR-Cas9 knockout experiments confirmed that SlIDI1 was the gene underlying the oft3 locus. qRT-PCR analysis revealed that the expression of SlIDI1 was highest in flowers and fruit and increased with fruit ripening or flower maturation. SlIDI1 simultaneously produced long and short transcripts by alternative transcription initiation and alternative splicing. Green fluorescent protein fusion expression revealed that the long isoform was mainly localized in plastids and that an N-terminal 59-amino acid extension sequence was responsible for plastid targeting. Short transcripts were identified in leaves and fruit by 5' RACE and in fruit by 3' RACE, which produced corresponding proteins lacking transit peptides and/or putative peroxisome targeting sequences, respectively. In SlIDI1 mutant fruit, SlBCH1 transcription involved in β-carotenoid catabolism was obviously suppressed, which may be responsible for the higher β-carotene-to-lycopene ratio and suggested potential feedback regulatory mechanisms involved in carotenoid pathway flux.
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Affiliation(s)
- Ming Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shaogui Guo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoliang Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Changbao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Wang X, Liu Z, Sun S, Wu J, Li R, Wang H, Cui X. SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato. HORTICULTURE RESEARCH 2021; 8:251. [PMID: 34848688 PMCID: PMC8633288 DOI: 10.1038/s41438-021-00677-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 05/19/2023]
Abstract
Selection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.
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Affiliation(s)
- Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiqiang Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianxin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haijing Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Chandrasekaran M, Boopathi T, Paramasivan M. A status-quo review on CRISPR-Cas9 gene editing applications in tomato. Int J Biol Macromol 2021; 190:120-129. [PMID: 34474054 DOI: 10.1016/j.ijbiomac.2021.08.169] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/09/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
Epigenetic changes are emancipated in horticultural crops including tomato due to a variety of environmental factors. These modifications rely on plant phenotypes mediated by genetic architecture consequently resulting in hereditary epigenetic memory. Genome editing strategies like CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/CRISPR-associated protein 9 (Cas9) technologies have revolutionized plants biology foreseeing stable inheritance of epigenetic modifications. CRISPR/Cas9 strategy poses as explicit advancement in providing precise genome editing with minimal off-target mutations, ease of experimental design, higher efficiency, versatility, and cost-effectiveness. Dicot crops, especially tomato remain an ideal candidate for CRISPR/Cas9 based gene modulations thereby augmenting productivity and yields. In the present review, key questions on CRISPR/Cas9 applications aid in enhanced growth based on optimal gene discovery, de novo modification, trait improvement, and biotic/abiotic stress management are discussed. In addition, comparative scenario in tomato and similar horticultural crops are adequately summarized for the pros and cons. Further, limitations hampering potential benefits and success phenomena of the lab to field transition of gene editing alterations are discussed collaterally in addressing futuristic optimization for CRISPR/Cas9 research in tomato.
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Affiliation(s)
- Murugesan Chandrasekaran
- Department of Food Science and Biotechnology, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea.
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Li G, Wang J, Zhang C, Ai G, Zhang D, Wei J, Cai L, Li C, Zhu W, Larkin RM, Zhang J. L2, a chloroplast metalloproteinase, regulates fruit ripening by participating in ethylene autocatalysis under the control of ethylene response factors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7035-7048. [PMID: 34255841 DOI: 10.1093/jxb/erab325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Although autocatalytic ethylene biosynthesis plays an important role in the ripening of climacteric fruits, our knowledge of the network that promotes it remains limited. We identified white fruit (wf), a tomato mutant that produces immature fruit that are white and that ripen slowly. We found that an inversion on chromosome 10 disrupts the LUTESCENT2 (L2) gene, and that white fruit is allelic to lutescent2. Using CRISPR/Cas9 technology we knocked out L2 in wild type tomato and found that the l2-cr mutants produced phenotypes that were very similar to white fruit (lutescent2). In the l2-cr fruit, chloroplast development was impaired and the accumulation of carotenoids and lycopene occurred more slowly than in wild type. During fruit ripening in l2-cr mutants, the peak of ethylene release was delayed, less ethylene was produced, and the expression of ACO genes was significantly suppressed. We also found that exogenous ethylene induces the expression of L2 and that ERF.B3, an ethylene response factor, binds to the promoter of the L2 gene and activates its transcription. Thus, the expression of L2 is regulated by exogenous ethylene. Taken together, our results indicate that ethylene may affect the expression of L2 gene and that L2 participates in autocatalytic ethylene biosynthesis during tomato fruit ripening.
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Affiliation(s)
- Guobin Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiafa Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunli Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dedi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wei
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangyu Cai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changbao Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wenzhao Zhu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
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Ji H, Mao H, Li S, Feng T, Zhang Z, Cheng L, Luo S, Borkovich K, Ouyang S. Fol-milR1, a pathogenicity factor of Fusarium oxysporum, confers tomato wilt disease resistance by impairing host immune responses. THE NEW PHYTOLOGIST 2021; 232:705-718. [PMID: 33960431 PMCID: PMC8518127 DOI: 10.1111/nph.17436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/14/2021] [Indexed: 05/03/2023]
Abstract
Although it is well known that miRNAs play crucial roles in multiple biological processes, there is currently no evidence indicating that milRNAs from Fusarium oxysporum f. sp. lycopersici (Fol) interfere with tomato resistance during infection. Here, using sRNA-seq, we demonstrate that Fol-milR1, a trans-kingdom small RNA, is exported into tomato cells after infection. The knockout strain ∆Fol-milR1 displays attenuated pathogenicity to the susceptible tomato cultivar 'Moneymaker'. On the other hand, Fol-milR1 overexpression strains exhibit enhanced virulence against the resistant cultivar 'Motelle'. Several tomato mRNAs are predicted targets of Fol-milR1. Among these genes, Solyc06g007430 (encoding the CBL-interacting protein kinase, SlyFRG4) is regulated at the posttranscriptional level by Fol-milR1. Furthermore, SlyFRG4 loss-of-function alleles created using CRISPR/Cas9 in tomato ('Motelle') exhibit enhanced disease susceptibility to Fol, further supporting the idea that SlyFRG4 is essential for tomato wilt disease resistance. Notably, our results using immunoprecipitation with specific antiserum suggest that Fol-milR1 interferes with the host immunity machinery by binding to tomato ARGONAUTE 4a (SlyAGO4a). Furthermore, virus-induced gene silenced (VIGS) knock-down SlyAGO4a plants exhibit reduced susceptibility to Fol. Together, our findings support a model in which Fol-milR1 is an sRNA fungal effector that suppresses host immunity by silencing a disease resistance gene, thus providing a novel virulence strategy to achieve infection.
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Affiliation(s)
- Hui‐Min Ji
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Hui‐Ying Mao
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Si‐Jian Li
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Tao Feng
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Zhao‐Yang Zhang
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Lu Cheng
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Shu‐Jie Luo
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
| | - Katherine A. Borkovich
- Department of Microbiology and Plant PathologyInstitute for Integrative Genome BiologyUniversity of California900 University AvenueRiversideCA92521USA
| | - Shou‐Qiang Ouyang
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJS225009China
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouJS225009China
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Two zinc-finger roteins control the initiation and elongation of long stalk trichomes in tomato. J Genet Genomics 2021; 48:1057-1069. [PMID: 34555548 DOI: 10.1016/j.jgg.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022]
Abstract
Plant glandular trichomes are epidermal secretory structures that are important for plant resistance to pests. Although several regulatory genes have been characterized in trichome development, the molecular mechanisms conferring glandular trichome morphogenesis are unclear. We observed the differences in trichomes in cultivated tomato cv. 'Moneymaker' (MM) and the wild species Solanum pimpinellifolium PI365967 (PP), and used a recombinant inbred line (RIL) population to identify the genes that control trichome development in tomato. We found that the genomic variations in two genes, H and SH, contribute to the trichome differences between MM and PP. H and SH encode two paralogous C2H2 zinc-finger proteins that function redundantly in regulating trichome formation. Loss-of-function h/sh double mutants exhibited a significantly decreased number of Type I trichomes and complete loss of long stalk trichomes. Molecular and genetic analyses further indicate that H and SH act upstream of ZFP5. Overexpression of ZFP5 partially restored the trichome defects in NIL-hPPshPP. Moreover, H and SH expression is induced by high temperatures, and their mutations inhibit the elongation of trichomes that reduce the plant repellent to whiteflies. Our findings confirm that H and SH are two vital transcription factors controlling initiation and elongation of Type I and III multicellular trichomes in tomato.
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Sami A, Xue Z, Tazein S, Arshad A, He Zhu Z, Ping Chen Y, Hong Y, Tian Zhu X, Jin Zhou K. CRISPR-Cas9-based genetic engineering for crop improvement under drought stress. Bioengineered 2021; 12:5814-5829. [PMID: 34506262 PMCID: PMC8808358 DOI: 10.1080/21655979.2021.1969831] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In several parts of the world, the prevalence and severity of drought are predicted to increase, creating considerable pressure on global agricultural yield. Among all abiotic stresses, drought is anticipated to produce the most substantial impact on soil biota and plants, along with complex environmental impacts on other ecological systems. Being sessile, plants tend to be the least resilient to drought-induced osmotic stress, which reduces nutrient accessibility due to soil heterogeneity and limits nutrient access to the root system. Drought tolerance is a complex quantitative trait regulated by multiple genes, and it is one of the most challenging characteristics to study and classify. Fortunately, the clustered regularly interspaced short palindromic repeat (CRISPR) technology has paved the way as a new frontier in crop improvement, thereby revolutionizing plant breeding. The application of CRISPER systems has proven groundbreaking across numerous biological fields, particularly in biomedicine and agriculture. The present review highlights the principle and optimization of CRISPR systems and their implementation for crop improvement, particularly in terms of drought tolerance, yield, and domestication. Furthermore, we address the ways in which innovative genome editing tools can help recognize and modify novel genes coffering drought tolerance. We anticipate the establishment of effective strategies of crop yield improvement in water-limited regions through collaborative efforts in the near future.
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Affiliation(s)
- Abdul Sami
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Zhao Xue
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Saheera Tazein
- Pgrl CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Arshad
- Plant Physiology Lab, Quaid I Azam University, Islamabad, Pakistan
| | - Zong He Zhu
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Ya Ping Chen
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Yue Hong
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Xiao Tian Zhu
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
| | - Ke Jin Zhou
- Rapeseed Cultivation and Breeding Lab, Anhui Agricultural University, Hefei, China
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Karavolias NG, Horner W, Abugu MN, Evanega SN. Application of Gene Editing for Climate Change in Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.685801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Climate change imposes a severe threat to agricultural systems, food security, and human nutrition. Meanwhile, efforts in crop and livestock gene editing have been undertaken to improve performance across a range of traits. Many of the targeted phenotypes include attributes that could be beneficial for climate change adaptation. Here, we present examples of emerging gene editing applications and research initiatives that are aimed at the improvement of crops and livestock in response to climate change, and discuss technical limitations and opportunities therein. While only few applications of gene editing have been translated to agricultural production thus far, numerous studies in research settings have demonstrated the potential for potent applications to address climate change in the near future.
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Xia X, Cheng X, Li R, Yao J, Li Z, Cheng Y. Advances in application of genome editing in tomato and recent development of genome editing technology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2727-2747. [PMID: 34076729 PMCID: PMC8170064 DOI: 10.1007/s00122-021-03874-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 05/07/2023]
Abstract
Genome editing, a revolutionary technology in molecular biology and represented by the CRISPR/Cas9 system, has become widely used in plants for characterizing gene function and crop improvement. Tomato, serving as an excellent model plant for fruit biology research and making a substantial nutritional contribution to the human diet, is one of the most important applied plants for genome editing. Using CRISPR/Cas9-mediated targeted mutagenesis, the re-evaluation of tomato genes essential for fruit ripening highlights that several aspects of fruit ripening should be reconsidered. Genome editing has also been applied in tomato breeding for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and recently customizing tomato cultivars for urban agriculture. In addition, genome editing is continuously innovating, and several new genome editing systems such as the recent prime editing, a breakthrough in precise genome editing, have recently been applied in plants. In this review, these advances in application of genome editing in tomato and recent development of genome editing technology are summarized, and their leaving important enlightenment to plant research and precision plant breeding is also discussed.
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Affiliation(s)
- Xuehan Xia
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xinhua Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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Abstract
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits include a series of backcrosses and selection to introduce beneficial traits into fine germplasm, this process is slow and resource-intensive. The new breeding technique known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9) has the potential to improve many traits rapidly and accurately, such as yield, quality, disease resistance, abiotic stress tolerance, and nutritional aspects in crops. Because of its simple operation and high mutation efficiency, this system has been applied to obtain new germplasm resources via gene-directed mutation. With the availability of whole-genome sequencing data, and information about gene function for important traits, CRISPR-Cas9 editing to precisely mutate key genes can rapidly generate new germplasm resources for the improvement of important agronomic traits. In this review, we explore this technology and its application in fruit and vegetable crops. We address the challenges, existing variants and the associated regulatory framework, and consider future applications.
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Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S, Ma W, She M. Application of CRISPR/Cas9 in Crop Quality Improvement. Int J Mol Sci 2021; 22:4206. [PMID: 33921600 PMCID: PMC8073294 DOI: 10.3390/ijms22084206] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.
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Affiliation(s)
- Qier Liu
- Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Fan Yang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Hang Liu
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shanjida Rahman
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Maoyun She
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
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50
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Genome editing in fruit, ornamental, and industrial crops. Transgenic Res 2021; 30:499-528. [PMID: 33825100 DOI: 10.1007/s11248-021-00240-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/25/2021] [Indexed: 01/24/2023]
Abstract
The advent of genome editing has opened new avenues for targeted trait enhancement in fruit, ornamental, industrial, and all specialty crops. In particular, CRISPR-based editing systems, derived from bacterial immune systems, have quickly become routinely used tools for research groups across the world seeking to edit plant genomes with a greater level of precision, higher efficiency, reduced off-target effects, and overall ease-of-use compared to ZFNs and TALENs. CRISPR systems have been applied successfully to a number of horticultural and industrial crops to enhance fruit ripening, increase stress tolerance, modify plant architecture, control the timing of flower development, and enhance the accumulation of desired metabolites, among other commercially-important traits. As editing technologies continue to advance, so too does the ability to generate improved crop varieties with non-transgenic modifications; in some crops, direct transgene-free edits have already been achieved, while in others, T-DNAs have successfully been segregated out through crossing. In addition to the potential to produce non-transgenic edited crops, and thereby circumvent regulatory impediments to the release of new, improved crop varieties, targeted gene editing can speed up trait improvement in crops with long juvenile phases, reducing inputs resulting in faster market introduction to the market. While many challenges remain regarding optimization of genome editing in ornamental, fruit, and industrial crops, the ongoing discovery of novel nucleases with niche specialties for engineering applications may form the basis for additional and potentially crop-specific editing strategies.
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