Integrated transcriptomic and metabolomic analyses revealed the role of SlMYC2 in tomato (Solanum lycopersicum L.) fruit development and ripening

Transcription factor (TF) MYC2 is a fundamental regulator of the jasmonic acid (JA) signaling pathway and has a role in plant development and stress regulation. However, a comprehensive understanding of MYC2 regulatory role in fruit development and ripening is still lacking. In this study, the integrative and comparative analysis was performed on the transcriptome and metabolome of wild-type (WT) and SlMYC2 knockout tomato fruit at mature green and red ripening stages to uncover the function of SlMYC2. A total of 764 metabolites and 30,280 annotated unigenes were identified. The differential accumulated metabolites (DAMs) and differentially expressed genes (DEGs) caused by SlMYC2 mutation were 32.3 % and 159.8 % higher in red ripening fruit than in mature green fruit, respectively. From the mature green to red ripening stages of tomato fruit, KEGG enrichment analysis revealed that the DEGs affected by SlMYC2 were primarily involved in photosynthesis, carbohydrate metabolism, phenylpropanoid pathway, carotenoid biosynthesis, and plant hormone signal transduction. In addition, there are 36 TFs families in these DEGs, mainly including MYB_related, MYB, bHLH, B3, ERF, NAC, HB-other, WRKY and bZIP. Furthermore, the co-expression and promoter analysis indicated that MYB44, PLA1, WRKY17, LOX2, PPA1-LIKE, JAZ, ACSL1 and PYL4 may play an important role in the aforementioned metabolic pathways regulated by SlMYC2. Overall, these findings indicate that many key metabolic pathways, transcription factors, and genes may be governed by SlMYC2, potentially being related to fruit development, ripening, quality and stress resistance mechanisms. This study provides new insights into the function of MYC2 and lays a foundation for further research on the molecular mechanism underlying fruit development and ripening.