Chemical Profiling of Wild and Commercial Tomato Leaves: Protocol Optimization, Insights into Differences in Chemical Profiles between Species and Developmental Stages

The tomato is a globally important crop whose domestication has led to significant chemical changes that may reduce its natural defenses. This study compares the chemical profiles of wild (Solanum pimpinellifolium) and commercial (Solanum lycopersicum, cultivar BRS Iracema) tomato leaves across three developmental stages: seedling, vegetative, and flowering. We used optimized ultrasound-assisted extraction for nonvolatile compounds and headspace extraction for volatile compounds. We coupled these methods with UHPLC-q-TOF-MS/MS and GC–MS to investigate their chemical composition. Multivariate analysis revealed that domestication profoundly altered chemical profiles, particularly affecting glycosylated alkaloids, phenylpropanoids, and gibberellins. During the seedling stage, S. pimpinellifolium exhibited higher accumulation of defense-related compounds, including alpha-tomatine and tomatidine. In contrast, the commercial species exhibited enhanced anthocyanin biosynthesis and higher levels of glyceric acid, particularly during the vegetative stage. Differences in specific compounds, such as 3-indoleacrylic acid, certain peptides, clausarinol, and gibberellin aldehyde A12, were also observed across developmental stages. While chemical profiles varied across developmental stages, the impact of domestication on the tomato chemical profile was generally more pronounced. These findings provide information for targeted breeding, such as the identification of key metabolites like alpha-tomatine and tomatidine that enhance stress resistance. The findings also help to identify the biosynthesis of anthocyanins and other compounds that improve the nutritional quality of cultivated tomato species.