Integrated Metabolome and Transcriptome Analysis Reveals Dynamic Changes in Flavonoid Accumulation and Pericarp at Different Sowing Dates in Sorghum

This study investigated the regulatory effects of sowing date on seed quality formation in the brewing sorghum cultivar Hongyingzi using integrated transcriptomic and metabolomic approaches. Three sowing dates (early, normal, and late) were applied, and seeds were collected at 19, 26, and 33 days after pollination. Sowing date interacted with seed development to significantly affect morphological characteristics, pericarp structure, and metabolite accumulation. Transcriptomic analysis identified 3651 shared differentially expressed genes (DEGs) mainly enriched in photosynthesis, starch and sucrose metabolism, and flavonoid biosynthesis. Metabolomic profiling detected 1105 differentially expressed metabolites (DEMs), which were involved in flavonoid and starch–sucrose metabolism. Integrated analysis confirmed these two pathways as key responses to sowing date. Weighted gene co-expression network analysis (WGCNA) identified 17 hub genes, five of which were upregulated and contained light-responsive elements. These findings reveal the molecular mechanism underlying sowing date-mediated seed quality formation and provide a theoretical basis for high-quality sorghum production.