Carotenoids are indispensable plant secondary metabolites that are involved in photosynthesis, antioxidation, and phytohormone biosynthesis. Carotenoids are likely involved in other biological functions that have yet to be discovered. In this study, we integrated genomic, biochemical, and cellular studies to gain deep insight into carotenoid-related biological processes in citrus calli overexpressing CrtB (phytoene synthase from Pantoea agglomerans). Fortunella hindsii Swingle (a citrus relative) and Malus hupehensis (a wild apple) calli were also utilized as supporting systems to investigate the effect of altered carotenoid accumulation on carotenoid-related biological processes. Transcriptomic analysis provided deep insight into the carotenoid-related biological processes of redox status, starch metabolism, and flavonoid/anthocyanin accumulation. By applying biochemical and cytological analyses, we determined that the altered redox status was associated with variations in O2 - and H2O2 levels. We also ascertained a decline in starch accumulation in carotenoid-rich calli. Furthermore, via an extensive cellular investigation of the newly constructed CrtB overexpressing Fortunella hindsii Swingle, we demonstrated that starch level reducation occurred in parallel with significant carotenoid accumulation. Moreover, studying anthocyanin-rich Malus hupehensis calli showed a negative effect of carotenoids on anthocyanin accumulation. In citrus, altered carotenoid accumulation resulted in dramatic effects on metabolic processes involved in redox modification, starch degradation, and flavonoid/anthocyanin biosynthesis. These findings provided new perspectives to understand the biological importance of carotenogenesis and of the developmental processes associated with the nutritional and sensory qualities of agricultural products that accumulate carotenoids.

Autopolyploidization is critical to plant evolution and breeding, but systematic studies on its effects in woody plants remain limited. To address this gap, a systematic investigation covering autopolyploidization-induced variations in two autotetraploid jujube cultivars and their diploid counterparts across morphological, cytological, and metabolic levels was conducted in the present study. Compared with the diploids, the autotetraploid jujubes exhibited larger leaves, flowers, and fruits, but a dwarfing phenotype with reduced fruit set. Additionally, decreased leaf stomatal density and weakened pollen viability were observed in the autotetraploid jujubes. Metabolomic analysis further revealed that autotetraploid fruits accumulated higher contents of soluble sugars, flavonoids, phenolics, and alkaloids but contained lower contents of amino acids. Based on LC-MS/MS quantification of leaf phytohormones, we identified six common hormones that were differentially accumulated in both cultivar comparisons. Notably, all six showed consistent alteration patterns between the two autotetraploid–diploid pairs. Together, these findings enhance our understanding of how autopolyploidy influences secondary metabolism, plant architecture, and hormone homeostasis in woody plants.