Comparative multi-omics reveals distinct transcriptomic and metabolomic profiles during fruit development in highbush and rabbiteye blueberries

Blueberry fruit quality is shaped by coordinated changes in gene expression and metabolite composition during development, but how these processes differ between cultivated blueberry species (highbush and rabbiteye) across developmental stages (green, pink and ripe) remains unclear. We integrated texture analysis, transcriptomics and metabolomics, to determine the contributions of developmental stage (green, pink, and ripe) and species differentiation to variation in transcriptomic and metabolomic profiles and fruit texture. Both factors influenced gene expression and metabolite accumulation. Transcriptomic and metabolomic analyses revealed strong species-associated variation, whereas developmental stage defined a conserved ripening trajectory. Across species, ripening was characterized by coordinated downregulation of photosynthesis pathways and increased accumulation of anthocyanins, flavonoids, phenolic acids, terpenoids, and carbohydrates. Species-associated differences remained across developmental stages: rabbiteye fruit exhibited higher expression of genes involved in stress responses, metabolite transport, and specialized metabolism, together with greater accumulation of phenylpropanoid derivatives and organic acids. In contrast, highbush fruit showed higher expression of genes associated with primary metabolism, nutrient transport, intracellular trafficking, and cell wall-related processes, accompanied by increased accumulation of flavonol glycosides, sphingolipids, and structural metabolites. Integrated multi-omics analyses identified key genes and metabolites for ripening and species, and their association with texture parameters. Candidate genes were prioritized through integration with previously reported genes involved in cell wall and lignin and flavonoid biosynthesis, providing potential targets for future functional characterization and marker -assisted breeding. Overall, developmental stage governs conserved ripening processes, whereas species-associated differences shape the transcriptomic and metabolomic landscape associated with fruit quality traits.