Genome-Wide and Co-Expression Network Dissection of PgUGT-Rd1 as a Central Regulator of Ginsenoside Rd Biosynthesis in Ginseng

Sizhang Liu^1*Meili Chi²Yi Wang³Meiping Zhang^3*

• ¹Changchun University of Chinese Medicine, Changchun, China
• ²National Ginseng Products Quality Supervision Inspection Center, Yanji, China
• ³Jilin Agricultural University, Changchun, China

Ginsenosides from Panax ginseng displayed diverse pharmacological activities, among which the protopanaxadiol-type ginsenoside Rd was particularly notable for its therapeutic potential. However, the mechanisms that governed its directed biosynthesis, as well as the key genes and regulatory networks involved, remained poorly defined. In this study, using a diverse panel of ginseng germplasm and integrating genome-Pwide association studies (GWAS), weighted gene co-expression network analysis (WGCNA), and additional multi-omics datasets, we systematically identified five candidate genes that were significantly associated with natural variation in Rd content. Among these, PgUGT-Rd1 exhibited strong co-expression with core enzyme-encoding genes in the ginsenoside biosynthetic pathway. Functional analyses revealed that methyl jasmonate (MeJA) treatment robustly induced PgUGT-Rd1 expression and concomitantly elevated Rd accumulation, whereas RNAi-mediated knockdown of PgUGT-Rd1 reduced Rd levels by approximately 50%. Together, these results established PgUGT-Rd1 as a key enzymatic node of the directed biosynthesis of Rd, providing new insights into the molecular mechanism of ginsenoside Rd biosynthesis.Our findings not only provided a framework for dissecting the regulatory architecture of ginsenoside biosynthesis in ginseng, but also delivered key molecular targets and markers for ginseng molecular breeding and ginsenoside metabolic engineering, and laid a conceptual and genetic foundation for the efficient and sustainable production of Rd.