Genetic Variability of Gene Expression in Tomato Fruits Ripened on and off the Vine: Cis-Regulatory Elements Associated with Differential Transcription Patterns in the Most Discrepant Variety

The cultivated tomato (<i>Solanum lycopersicum</i> L.) is a self-pollinating species whose fruit ripening is crucial for commercial quality, as many attributes are established during this stage. Fruits ripened on the plant usually have better quality than those ripened off the plant. This study combines traditional molecular techniques (cDNA-AFLP) with bioinformatics tools (PlantCARE and PLACE) to analyze gene expression in fruits ripened on the plant and off the plant from both cultivated and wild genotypes, which differ in shelf life. The goal is to analyze genetic variability in ripening-related transcripts at both ripening conditions and, once identified, the most discrepant variety, to characterize its cis-regulatory elements in the 5' DNA regions inducing differentially expressed genes. Results revealed wide genetic variability in gene expression according to differentially cDNA-AFLP amplicons detected in both ripening conditions. A strong association among the expressed genes under both ripening conditions and the phenotypic fruit traits related to post-harvest life was found. Though wild genotypes showed the greatest number of amplicons, the most discrepant genotype was the cultivated variety of standard shelf life. The analysis of the promoter in this genotype showed differences in cis-elements between conditions. In shelf-ripened fruits, stress-related elements were predominant and located near the transcription start site, whereas in on-plant ripening fruits, cis-motifs were more abundant farther from the start site. This research provides initial insights into the transcriptional networks regulating ripening and stress responses, offering valuable information for future genetic improvements and post-harvest strategies in tomato cultivation.