Multi-omics dissection of metabolic pathways for differential flavonoid accumulation in Solanum pennellii and S....

Our integrated multi-omics approach (transcriptomics, metabolomics, and mGWAS) indicated that differential expression of flavonoid biosynthesis genes may contribute to the differential flavonoid accumulation between wild and cultivated tomatoes. Tomato (Solanum lycopersicum) is a globally important vegetable crop and a foundational model for studying fruit development and metabolic regulation. Differential accumulation of metabolites such as flavonoids in wild and cultivated tomato fruits contributes to the differences in fruit flavor and nutritional quality. However, the loci and candidate genes regulating this accumulation remain largely unknown. To identify these loci and candidate genes, we performed integrated transcriptomic and metabolomic profiling of the cultivated tomato S. lycopersicum and wild tomato S. pennellii at the breaker and ripe stages. Comparative transcriptomics showed that differentially expressed genes between the two accessions were significantly enriched in biological processes such as glycosyl transfer. KEGG pathway enrichment analysis further highlighted the central role of flavonoid biosynthesis during fruit ripening. By constructing a co-expression network, we identified gene modules significantly correlated with the accumulation of flavonoid metabolites. A metabolite-based genome-wide association study (mGWAS) using an introgression line population mapped 21 genetic loci associated with flavonoid content. Multi-omics data integration suggested UGT73C4 as one of several possible candidate genes for naringin accumulation. Finally, a genome-wide evolutionary analysis of the UGT gene family across 27 Solanaceae species provided phylogenetic context for functional classification. The overall purpose of this multi-omics integration was to systematically characterize the flavonoid metabolic network in tomato and to prioritize UGT73C4 as a candidate gene potentially associated with naringin accumulation. Our findings contribute to the understanding of metabolic diversity and provide candidate genetic resources and a preliminary theoretical framework for targeted quality improvement in tomato breeding.