Metabolomics combined with transcriptomics reveals the accumulation mechanism of the fruit pulp colour of Baccaurea ramiflora Lour

Baccaurea ramiflora Lour., a wild fruit tree with edible, ornamental, and medicinal qualities. The mechanism behind the color accumulation in its fruit pulp, which can be either pink or milky-white, remains unclear. This study investigates the metabolome and transcriptome of two B. ramiflora pulp types—LR (milky-white at maturity) and BR (pink at maturity)—to elucidate their coloration processes. We identified 35 flavonoids, including nine involved in the anthocyanin synthesis pathway, confirming cyanidin as the pivotal pigment for the pink pulp coloration. An examination of the flavonoid and anthocyanin biosynthetic pathways in B. ramiflora pulp uncovered 38 differentially expressed genes associated with structural genes. The genes F3′5′H and UFGT exhibited high expression levels in the first two developmental stages of BR, significantly more than in LR, and were almost non-existent in later stages, signifying their crucial role in the differential color accumulation between BR and LR pulps. Additionally, the expression levels of CHI and FLS , early-stage structural genes in the anthocyanin synthesis pathway, correlated with the concentrations of naringenin and quercetin, indicating their importance in the anthocyanin biosynthesis pathway of B. ramiflora pulp. These discoveries provide new insights that could facilitate the breeding of B. ramiflora varieties with diverse pulp colors.