Comparative Metabolomic and Transcriptomic Analyses Identify Candidate Genes Associated with Flavonoid Accumulation and Phenylpropanoid Metabolism in Large-Fruited Hawthorn (Malus doumeri (Bois) Chev.)

Large-fruited hawthorn (Malus doumeri (Bois) Chev.) is valued for its health-promoting properties, largely attributed to its rich flavonoid content. However, little is known about the specific composition of flavonoids and the molecular mechanisms regulating their biosynthesis. The present study employed non-targeted metabolomic and transcriptomic approaches to investigate two M. doumeri germplasms (G8 and G9) that exhibited significantly different total flavonoid contents. The results indicated that the major and differential metabolites primarily include flavonoids and isoflavonoids. Differentially expressed genes were significantly enriched in phenylpropanoid and flavone and flavonol biosynthesis pathways. Integrated analysis identified several structural genes and transcription factors, including HCT (LOC114821133, LOC103403337, LOC103454980), WRKY (LOC103427630), and bHLH (LOC103422512), that were significantly upregulated in the high-flavonoid genotype (G9). qRT-PCR validation confirmed the RNA-Seq expression patterns, suggesting the potential involvement of these genes in the biosynthesis of phenylpropanoid-related metabolites, such as [6]-gingerol. Applied experiments further demonstrated that freeze-drying preserved high metabolite contents and antioxidant activity. Collectively, these findings provide insights into the compositional characteristics of the major flavonoids in M. doumeri and the biosynthesis of phenylpropanoid-derived metabolites. This study provides data support for future mechanistic validation and evaluation of processing technology applicability.