## 1 Introduction  
Fruit ripening is a complex developmental process that entails dramatic changes in color, texture, flavor, and aroma. These changes are tightly regulated by a network of transcription factors (TFs) that orchestrate the expression of the genes involved in various metabolic pathways [1]. Understanding the regulatory mechanisms underlying fruit ripening is crucial for developing strategies towards fruit quality improvement and shelf-life extension.  
The NF-Y family TFs have been known to affect a vast range of biological processes (BP), from flowering to abiotic stress tolerance. In tomato, evidence suggests that they affect multiple fruit characteristics in terms of the quality, color, and flavonoid biosynthesis [2]. The NF-Y family comprises highly conserved proteins that modulate gene expression in a heterotrimer fashion. The three subunits NF-YA, NF-YB, and NF-YC form a complex that binds to the CCAAT box in the promoter regions of genes [3], while the target gene specificity of the complex to target genes can also be synergistically influenced by other TFs, such as basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) [4; 5]. The NF-Y family members are crucial master regulators of multiple downstream genes and BP, controlling agronomic traits that are important breeding targets. For instance, NF-YA8 coordinates the developmental aspects that can influence cotyledon growth, stem structure, inflorescence design, flowering timing, fruit size, and shape. Interestingly, the disruption of NF-YA8 had a substantial impact on a fruit's morphology, its overall shape, dimensions, weight, spal number, and fruit angle ratios [6].  
In our previous studies, we employed a targeted gene disruption workflow on the NF-YB family member LEAFY COTYLEDON1-LIKE4 (L1L4 or NF-YB6), a known master regulator of fatty acid biosynthesis and seed storage proteins. Aside from its involvement in various aspects of plant development [7], expression in flowers, and unripe tomato fruits [8], we additionally investigated its influence on the metabolic profiles of tomato fruit [9]. Notably, the _I114_ mutant lines showcased subtle differences in terms of the fruit size compared to the wild-type (WT) line, followed by significant changes in the fruit's physiological parameters (e.g., moisture content, titratable acidity, etc.) and metabolic profiles (e.g., total polyphenols, antioxidants, oxalic and citric acid, fructose, and \(\beta\)-carotene). These altered metabolic profiles were also evident in seeds, showcasing a substantial variability in bioactive compounds compared to the WT seeds.  
In this study, we further explored L1L4's critical regulatory role as an NF-YB TF in the modulation of a wide network of genes, which can eventually affect various complex processes occurring in tomato fruit. For our analysis, we compared the fruit transcriptomes of two previously generated _I114_ mutant lines (M7_5 and M29_2), both known for their distinct physiological and metabolic profiles compared to the WT, specifically regarding fruit fructose content, organic acid profiles, phenol content, and antioxidant activity. Our findings provide insights into the role of L1L4 in regulating fruit quality and metabolism in tomatoes, showcasing the vast effects of L1L4 in regulating downstream processes that involve a multitude of genes, epigenetic regulators, and TFs. Overall, this study aims to contribute valuable insights towards the development of elite tomato varieties.