Dynamic distribution and biosynthesis of bioactive compounds: Determining factors for their content in Rubus chingii fruit

Rubus chingii, is renowned for its dietary and medicinal properties. The fruit's flavonoids and ellagic acid/ellagitannins are essential for its taste, flavor, and pharmaceutical applications. This study investigates these phytochemicals across fruit tissues, maturation stages, and a germplasm collection using mass spectrometry imaging (MALDI-TOF IMS) and tandem mass spectrometry (MS/MS). Furthermore, we integrated transcriptomic data and qPCR to explore the relationship between key biosynthetic genes. As a result, kaempferol aglycones were predominantly accumulated in the drupelets, while anthocyanins, quercetin aglycones, and ellagic acid/ellagitannins were primarily in the receptacle. Also, kaempferol aglycones were accumulated in numerous hairs attached to the outer layer of the drupelet. These compounds were the most abundant at the mature green stage (MG, the earliest stage of maturity) and decreased with fruit maturation in both drupelets and receptacles. In the flavonoid pathway, the key genes, RchFLS, had a higher expression in drupelets than in the receptacle, but conversely, RchDRF had a higher expression in the receptacle than in drupelets. In the ellagic acid pathway, the rate-limiting gene RchGT2 had a higher expression in receptacles than in drupelets. Their different expressions between drupelets and receptacles were responsible for the uneven distribution of these flavonoids and ellagic acid/ellagitannins. Moreover, the expression of these genes was almost downregulated as the fruit matured, which was associated with a decline in flavonoids and ellagic acid/ellagitannin. Fruit shape index (FSI) reflecting the proportion of the receptacle was positively correlated with total ellagic acid content in the fruits (R = 0.704, P < 0.0001). These findings could help breeders easily improve cultivars for pharmaceutical value with morphological selection, and producers harvest fruits at the right time for either medicinal purposes or the food market.