Targeted Metabolite and Gene Expression Analysis of Anthocyanin and Kaempferol Glycoside Accumulation in Peach Accessions with Contrasting Flesh and Skin Pigmentation

Peach (Prunus persica) fruit pigmentation is largely associated with anthocyanin accumulation, whereas colorless flavonols such as kaempferol glycosides may reflect alternative use of shared flavonoid precursors. To examine the relationship between anthocyanin and selected kaempferol glycoside accumulation, we analyzed 15 peach accessions classified by red, white, or yellow flesh pigmentation. Skin color was quantified using the a*/b* ratio, where a* represents redness/greenness and b* represents yellowness/blueness. Red-fleshed accessions showed higher skin a*/b* values and accumulated higher levels of total anthocyanins, particularly cyanidin-3-glucoside, than white and yellow accessions. In contrast, kaempferol-3-rhamnoside preferentially accumulated in white-fleshed accessions. Expression analysis of flavonoid pathway genes showed that dihydroflavonol 4-reductase (PpDFR) was more highly expressed in red accessions, whereas flavonol synthase (PpFLS) was more highly expressed in white accessions; chalcone synthase (PpCHS), flavanone 3-hydroxylase (PpF3H), flavonoid 3′-hydroxylase (PpF3′H), and anthocyanidin synthase (PpANS) showed no significant differences among color groups. Heterologous overexpression of PpF3′H in Arabidopsis thaliana, a well-characterized model plant for flavonoid biosynthesis, was associated with increased seed anthocyanin accumulation and a lower kaempferol-to-quercetin ratio, supporting its catalytic capacity to influence flavonoid composition in an exogenous system. Overall, these results indicate that differential anthocyanin and selected kaempferol glycoside accumulation in peach is associated with the relative expression patterns of branch-related flavonoid genes, particularly PpDFR and PpFLS. This study provides targeted metabolic and transcriptional evidence for understanding peach flesh and skin pigmentation and provides mechanistic insight into flavonoid branch competition linking gene expression patterns with metabolite allocation, and identifies candidate genes for improving fruit color and flavonoid-related nutritional quality.