Integrative Transcriptomic and Metabolomic Analyses Reveal Flavonoid Accumulation Characteristics in the Flesh of Red-Fleshed Grape and Self-Pollinated Progenies

This study investigated differences in flavonoid-related gene expression and metabolite profiles in the flesh of red-fleshed grape berries and their self-pollinated progenies, aiming to elucidate the metabolic accumulation characteristics of flavonoid biosynthesis, and provide insights into transcriptional regulation, so as to lay a theoretical foundation for improving flavonoid contents in grape berries and breeding new grape varieties.

The red-fleshed grape germplasm Zhongshanhongyu (ZSHY), its self-pollinated progenies Nan 19 (N19) and Nan 30 (N30), and Muscat (MGX) were used as materials. Four pairwise comparison groups (ZSHY_vs_MGX, N30_vs_ZSHY, N19_vs_MGX, and N30_vs_N19) were established for targeting flavonoid metabolomics alongside transcriptome sequencing (RNA-seq) of berry flesh. Enrichment analyses were subsequently conducted to characterize flavonoid metabolites accumulation, identify key structural genes, and dissect the transcriptional regulatory networks involved in flavonoid biosynthetic pathway.

Based on targeted flavonoid metabolomics technology, a total of 104 differentially accumulated flavonoid metabolites were detected, and 62 core metabolites exhibiting significant differences were further identified. Notably, most flavonols and flavanols accumulated to substantially higher levels in ZSHY and N19 than in N30 and MGX. KEGG enrichment analysis revealed that these differential metabolites were predominantly enriched in flavonoid biosynthesis pathways, particularly responsible for anthocyanin, flavone, and flavonol biosynthesis. Transcriptome profiling identified 758 differentially expressed genes (DEGs), which were significantly overrepresented in flavonoid and phenylpropanoid biosynthesis pathways. Furthermore, 30 core DEGs directly involved in flavonoid biosynthesis were screened, whose expression patterns were broadly consistent with the metabolite accumulation profiles, showing high transcript abundance in ZSHY and N19, but low expression in N30 and MGX. In addition, 22 transcription factors (TFs) significantly correlated with flavonoid structural genes were identified, mainly belonging to the WRKY, MYB, and ERF families.

Significant differences existed in flavonoid metabolism between the red-fleshed grape and its self-pollinated progenies. The elevated flavonoid accumulation in the flesh of ZSHY and N19 was closely associated with the upregulation of the key structural genes in the flavonoid pathway, and the identified TFs might play important regulatory roles in this process.