Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.

Targeted genome editing using CRISPR/Cas nucleases has become the standard approach for creating mutant plants. Significant progress has been made to enhance the editing efficiencies through optimizing CRISPR/Cas expression, including applying heat stress. In this study, we used heat stress to enhance the Potato virus X (PVX)-mediated CRISPR/Cas9 mutagenesis in Nicotiana benthamiana. We show that heat stress at 4-5 days after PVX inoculation effectively increases the mutagenesis efficiency of Cas9 nuclease. We observed up to a 5-8% increase in mutation efficiency depending on the sgRNA construct when heat stress is applied to the pPVX-Cas9::sgRNA infiltrated samples. Furthermore, analysis of the effect of the heat stress on the pattern of mutation types in the target gene regions showed no obvious changes in CRISPR/Cas9 induced mutagenesis pattern between heat stress treated and no heat stress treated samples. Overall, our experiments demonstrate that heat stress treatment at the optimal time after viral inoculation is most effective in increasing the PVX-mediated CRISPR/Cas9 editing efficiency in plants.

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Citations to this article as recorded by  

• Exogenous melatonin enhances heat stress tolerance in sweetpotato by modulating antioxidant defense system, osmotic homeostasis and stomatal traits
  Sunjeet Kumar, Rui Yu, Yang Liu, Yi Liu, Mohammad Nauman Khan, Yonghua Liu, Mengzhao Wang, Guopeng Zhu
  Horticultural Plant Journal.2025; 11(1): 431.     CrossRef
• Broadening the Nicotiana benthamiana research toolbox through the generation of dicer-like mutants using CRISPR/Cas9 approaches
  Eirini Bardani, Konstantina Katsarou, Eleni Mitta, Christos Andronis, Marie Štefková, Michael Wassenegger, Kriton Kalantidis
  Plant Science.2025; 356: 112490.     CrossRef
• Development of virus-induced genome editing methods in Solanaceous crops
  Seo-Young Lee, Bomi Kang, Jelli Venkatesh, Joung-Ho Lee, Seyoung Lee, Jung-Min Kim, Seungki Back, Jin-Kyung Kwon, Byoung-Cheorl Kang
  Horticulture Research.2024;[Epub]     CrossRef
• Considerations in engineering viral vectors for genome editing in plants
  Xiaoyun Wu, Ying Zhang, Xue Jiang, Tingshuai Ma, Yating Guo, Xiaoxia Wu, Yushuang Guo, Xiaofei Cheng
  Virology.2024; 589: 109922.     CrossRef
• CRISPR/Cas9-gene editing approaches in plant breeding
  Himanshu Saini, Rajneesh Thakur, Rubina Gill, Kalpana Tyagi, Manika Goswami
  GM Crops & Food.2023; 14(1): 1.     CrossRef

Crop improvement is essential to attaining world food security and enhancing nutrition for human beings. Both conventional breeding and modern molecular breeding have contributed to increased crop production and quality. However, the time and resources for breeding practices have been limited. It takes a long time to bring a novel improved crop to the market, and the genetic sources from wild species cannot be always available for crops of our interests. Genome editing technology implemented molecular breeding can overcome those limitations of time and resource by facilitating the specific editing of plant genomes. However, there is a long-lasting argument about the safety of genetically modified organisms (GMOs). In this review, we briefly summarize the principle of genome editing tools, focusing on the CRISPR/Cas9 system and the application of these tools to plants in the service of crop engineering.

Citations

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• Drought-Tolerant Biotech Soybean Breeding in South America: Current Status, Commercialization, and Implications for Korea’s Technology Export Strategy
  Seung Young Choi, Yong Hun Song, Seung Muk Won, Kyeong Hee Lee, Ga Ram Kim, Taeyoung Um
  Korean Journal of Breeding Science.2026; 58(1): 13.     CrossRef
• Enhancing barley resilience: advanced genetic techniques to improve drought tolerance for sustainable cultivation under current climatic fluctuations
  Fatmah A. Safhi
  Cereal Research Communications.2025; 53(1): 17.     CrossRef
• An Efficient Protoplast Isolation Method Using Hypocotyl in Soybean (Glycine max)
  Jaehwan Kim, Yeong Yeop Jeong, Hyunwoo Park, Pil Joon Seo, Kyung Do Kim
  Korean Journal of Breeding Science.2025; 57(1): 1.     CrossRef
• Precision Breeding in Fruit Crops
  Shikha Jain, Jai Prakash
  RASSA Journal of Science for Society.2024; 6(1): 31.     CrossRef
• Combination of Hairy Root and Whole-Plant Transformation Protocols to Achieve Efficient CRISPR/Cas9 Genome Editing in Soybean
  Qihui Kong, Jie Li, Shoudong Wang, Xianzhong Feng, Huixia Shou
  Plants.2023; 12(5): 1017.     CrossRef
• Research Advances in Wheat Breeding and Genetics for Powdery Mildew Resistance
  Myoung-Hui Lee, Sumin Hong, Kyeong-Min Kim, Yurim Kim, Sun-Hwa Kwak, Kyeong-Hoon Kim, Chon-Sik Kang, Chul Soo Park, Youngjun Mo, Changhyun Choi
  Korean Journal of Breeding Science.2023; 55(3): 218.     CrossRef
• Quality trait improvement in horticultural crops: OMICS and modern biotechnological approaches
  Tanzeel Bashir, Syed Anam Ul Haq, Salsabeel Masoom, Mwafaq Ibdah, Amjad M. Husaini
  Molecular Biology Reports.2023; 50(10): 8729.     CrossRef
• Application of CRISPR/Cas9 technology to improve the important traits in coffee
  T J Santoso, A Sisharmini, Syafaruddin
  IOP Conference Series: Earth and Environmental Science.2022; 974(1): 012082.     CrossRef
• Enhancing plant immunity by expression of pathogen-targeted CRISPR-Cas9 in plants
  Hong Gil Lee, Duk Hyoung Kim, Yee-Ram Choi, Jihyeon Yu, Sung-Ah Hong, Pil Joon Seo, Sangsu Bae
  Gene and Genome Editing.2021; 1: 100001.     CrossRef
• Fruit crops in the era of genome editing: closing the regulatory gap
  Derry Alvarez, Pedro Cerda-Bennasser, Evan Stowe, Fabiola Ramirez-Torres, Teresa Capell, Amit Dhingra, Paul Christou
  Plant Cell Reports.2021; 40(6): 915.     CrossRef
• Nanoscale Drug Delivery Systems: From Medicine to Agriculture
  Pablo Vega-Vásquez, Nathan S. Mosier, Joseph Irudayaraj
  Frontiers in Bioengineering and Biotechnology.2020;[Epub]     CrossRef
• Facilitated adaptation for conservation – Can gene editing save Hawaii's endangered birds from climate driven avian malaria?
  Michael D. Samuel, Wei Liao, Carter T. Atkinson, Dennis A. LaPointe
  Biological Conservation.2020; 241: 108390.     CrossRef
• Antinutrients in Plant-based Foods: A Review
  Aneta Popova, Dasha Mihaylova
  The Open Biotechnology Journal.2019; 13(1): 68.     CrossRef
• Effect of phosphate nutrition on growth, physiology and phosphate transporter expression of cucumber seedlings
  Zakira Naureen, Arjun Sham, Hibatullah Al Ashram, Syed A. Gilani, Salma Al Gheilani, Fazal Mabood, Javid Hussain, Ahmed Al Harrasi, Synan F. AbuQamar
  Plant Physiology and Biochemistry.2018; 127: 211.     CrossRef
• A simple, flexible and high‐throughput cloning system for plant genome editing via CRISPR‐Cas system
  Hyeran Kim, Sang‐Tae Kim, Jahee Ryu, Min Kyung Choi, Jiyeon Kweon, Beum‐Chang Kang, Hyo‐Min Ahn, Suji Bae, Jungeun Kim, Jin‐Soo Kim, Sang‐Gyu Kim
  Journal of Integrative Plant Biology.2016; 58(8): 705.     CrossRef
• Is there a future for genome-editing technologies in conservation?
  J. A. Johnson, R. Altwegg, D. M. Evans, J. G. Ewen, I. J. Gordon, N. Pettorelli, J. K. Young
  Animal Conservation.2016; 19(2): 97.     CrossRef