Expression dynamics of starch and proanthocyanidin biosynthesis genes during Quercus glauca fruit development

BACKGROUND: Acorns are nutrient-rich fruits in which starch and proanthocyanidins (PAs) constitute the two dominant storage and defense metabolites. Transcriptomic studies in oaks have focused on stress responses, cork formation, and somatic embryogenesis, while omics and metabolic studies of acorn development remain scarce. We hypothesized that starch and PA biosynthesis in Quercus glauca fruits are governed by stage-specific transcriptional programs that drive their differential accumulation during fruit maturation. RESULTS: In this study, we utilized transcriptome data to investigate the expression dynamics of genes associated with starch and PA biosynthesis during Quercus glauca fruit development. Starch content increased continuously from 5.0 to 9.5 mg/mg protein across the five developmental stages of Q. glauca fruit, whereas PA content fluctuated within 0.015-0.038 mg/mg protein, peaking at T3 and T5. Transcriptome sequencing identified 2,637 differentially expressed genes (DEGs), predominantly partitioned into the rapid fruit growth phase (T3-T5) and enriched in PA biosynthesis, sugar metabolism, seed germination, and cell-cycle processes. Weighted gene co-expression network analysis (WGCNA) identified five modules significantly correlated with starch or PA content, within which 50 hub genes including QgPAL7 were identified. Mfuzz clustering showed PA biosynthesis genes were induced early and progressively repressed toward maturation, whereas starch biosynthesis genes were continuously up-regulated. WGCNA co-expression and metabolite-correlation analyses identified QgMYB33 as a stage-specific candidate associated with both PA and starch biosynthesis. The GPT family exhibited expansion through both tandem and segmental duplications. RT-qPCR validation of nine selected genes confirmed the RNA-seq expression patterns. CONCLUSION: This study characterizes a biphasic transcriptional program coordinating starch and PA biosynthesis during Q. glauca fruit development and identifies QgGPT7, QgGPT10, QgPAL7 and QgMYB33 as candidates, providing a molecular foundation for the future utilization and improvement of acorn resources.