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.

Senescence, a crucial developmental process in the life cycle of plants, involves programmed destruction of cellular components of leaves. The onset of senescence is synchronized with other developmental processes for successful reproduction since senescence eventually leads to cell death. Arabinosyltransferase FASCIATED AND BRANCHED 2 (FAB2) is known to control meristem proliferation. Here, we show that FAB2 could inhibit premature leaf senescence in tomato plants. Both chemically mutagenized and CRISPR-generated fab2 mutants exhibited excessively accelerated senescence, which resulted in sterility. Transcriptome analysis revealed that FAB2 extended leaf longevity by suppressing transcription of genes highly expressed in mature leaves. Transcription of FAB2 was increased in younger leaves, potentially inhibiting premature leaf senescence. The precocious senescence of fab2 mutants was in contrast to fasciated inflorescence (fin) mutants, which carried mutations in a hydroxyproline O-arabinosyltransferase gene, leading to meristem overproliferation. Our observations indicate that complex genetic hierarchy in the cascade of tomato arabinosyltransferases could control different aspects of developmental processes such as stem cell proliferation and senescence.