Two-phase regulatory mechanism of cyanidin glycosides drives fruit color differentiation in Camellia chekiangoleosa Hu. pericarp: A multi-omics study for pigment valorization

The pericarp of Camellia chekiangoleosa Hu. is a promising source of natural pigments for industrial applications. However, its comprehensive utilization remains very limited, and the fruit is largely discarded as processing waste. Understanding the mechanisms underlying pigment formation in this species is therefore of considerable value for unlocking the potential of this pigment-rich resource. In this study, we first analyzed the pigments in mature fruit pericarps displaying red, yellow, and green colors. We then performed integrated anthocyanin metabolomic and transcriptomic analyses on red and green fruits across six developmental stages. The results demonstrated that flavonoids are the primary compounds driving fruit color differentiation in C. chekiangoleosa . Three cyanidin glycosides were identified as responsible for the red coloration, and their accumulation followed a distinct "bimodal" pattern during fruit development, revealing a two-phase regulatory mechanism. Temporal changes in the expression of differentially expressed genes within the anthocyanin biosynthetic pathway are linked to the development of the red fruit phenotype. Weighted gene co-expression network analysis further identified seven key candidate genes significantly associated with anthocyanin accumulation, including Cole03G002063 (FLS) , Cole02G001539 (DFR) , and Cole13G001804 (ANS) . Additionally, we propose a novel “dual-block” hypothesis to explain the formation of yellow fruits—a phenotype arising from the concurrent suppression of chlorophyll degradation and anthocyanin biosynthesis. Collectively, these findings provided a theoretical foundation for utilizing pericarp pigments as bio-based industrial products and for molecular breeding programs targeting fruit color traits in this industrial crop.