Genome-wide and co-expression network dissection of

Introduction: Ginsenosides from Panax ginseng represent a major class of triterpenoid saponins with important biological activities, among which the protopanaxadiol-type ginsenoside Rd is of particular interest. Despite advances in ginsenoside research, the genetic basis and regulatory framework underlying directed Rd biosynthesis remain largely unresolved. Methods: Here, we integrated genome-wide association studies (GWAS), weighted gene co-expression network analysis (WGCNA), and multi-omics datasets across a diverse ginseng germplasm panel to identify candidate genes associated with natural variation in Rd accumulation. Expression profiling, methyl jasmonate (MeJA) induction assays, and RNA interference (RNAi)-mediated functional validation were employed to characterize the role of the key candidate gene PgUGT-Rd1 within the ginsenoside biosynthetic network. Results: Five candidate genes were identified as significantly associated with Rd content. PgUGT-Rd1 displayed strong co-expression with core enzymatic genes involved in triterpenoid saponin biosynthesis. MeJA treatment markedly induced PgUGT-Rd1 expression and enhanced Rd accumulation, whereas RNAi-mediated silencing of PgUGT-Rd1 resulted in an approximately 50% reduction in Rd levels, demonstrating its functional contribution to Rd biosynthesis. Discussion: Our findings establish PgUGT-Rd1 as an important UDP-glycosyltransferase associated with the directed biosynthesis of ginsenoside Rd and provide new insights into the regulatory architecture of ginsenoside metabolic pathways in ginseng. This integrative framework highlights candidate molecular targets for precision breeding and metabolic engineering and advances the understanding of specialized metabolism in medicinal plants.