Jeon, Yu-Jin Hong, Seungpyo Lee, Taek Sung Park, Soo Hyun Song, Giha Seo, Myeong-Gyun Lee, Jiwoo Lim, Yoonseo An, Jeong-Tak Lee, Sehee Jeong, Ho-Young Park, Soon Ju Lee, Chanhui Jung, Dae-Hyun Kwon, Choon-Tak 2025-08-26T02:30:30Z 2025-08-26T02:30:30Z 2025-08-23 2025-09 2643-6515 https://pubs.kist.re.kr/handle/201004/153038 Global climate change and urbanization have posed challenges to sustainable food production and resource management in agriculture. Vertical farming, in particular, allows for high-density cultivation on limited land but requires precise control of crop height to suit vertical farming systems. Tomato, a globally significant vegetable crop, urgently requires mutant varieties that suppress indeterminate growth for effective cultivation in vertical farming systems. In this study, we utilized the CRISPR-Cas9 system to develop a new tomato cultivar optimized for vertical farming by editing the Gibberellin 20-oxidase (SlGA20ox) genes, which are well known for their roles in the “Green Revolution”. Additionally, we proposed a volumetric model to effectively identify mutants through non-destructive analysis of chlorophyll fluorescence. The proposed model achieved over 84 ​% classification accuracy in distinguishing triple-determinate and slga20ox gene-edited plants, outperforming traditional machine learning methods and 1D-CNN approaches. Unlike previous studies that primarily relied on manual feature extraction from chlorophyll fluorescence data, this research introduced a deep learning framework capable of automating feature extraction in three dimensions while learning the temporal characteristics of chlorophyll fluorescence imaging data. The study demonstrated the potential to classify tomato plants customized for vertical farming, leveraging advanced phenotypic analysis methods. Our approach explores new analytical methods for chlorophyll fluorescence imaging data within AI-based phenotyping and can be extended to other crops and traits, accelerating breeding programs and enhancing the efficiency of genetic resource management. English American Association for the Advancement of Science Volumetric Deep Learning-Based Precision Phenotyping of Gene-Edited Tomato for Vertical Farming Article 10.1016/j.plaphe.2025.100095 1 Plant Phenomics, v.7, no.3 Plant Phenomics 7 3 Y scie scopus 001658238300001 Agronomy Plant Sciences Remote Sensing Agriculture Plant Sciences Remote Sensing Article CHLOROPHYLL-A FLUORESCENCE GREEN-REVOLUTION GIBBERELLIN BIOSYNTHESIS ROC CURVE COMPONENTS GROWTH 3D-CNN Tomato CRISPR-Cas9 Gibberellin Chlorophyll fluorescence imaging