ABSTRACT: Fruit flavor and color are critical quality characteristics of tomatoes. Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analyses were conducted on the closely related yellow-fruited tomato (No.19) and red-fruited tomato (No.20) strains. This analysis aimed to identify key regulatory genes and biosynthetic pathways related to flavor and color development in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the differentially expressed genes, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide insights into the underlying mechanisms of flavor and color development in tomato fruit, offering valuable information for the genetic improvement of tomatoes.
