Transcriptional regulation of polyphyllin biosynthesis of Paris polyphylla in response to soil moisture stress

Soil moisture critically regulates plant growth and bioactive compound in medicinal plants, yet its role in balancing these processes under drought remains unclear. This study investigates the effects of three soil moisture levels (40 %, 55 %, and 70 % soil water content: SWC40, SWC55, SWC70) on the growth and polyphyllin biosynthesis of Paris polyphylla . Results demonstrated that SWC40 significantly delayed seedling sprouting and leaf expansion compared to SWC55 and SWC70, while concurrently enhancing polyphyllin accumulation in the rhizomes. Transcriptomic analysis identified 40 differentially expressed genes associated with polyphyllin biosynthesis. Most of the genes were significantly highly expressed in the rhizomes under SWC40, consistent with the elevated polyphyllin content. Co-expression network analysis revealed drought-responsive transcription factors, including basic leucine zipper (bZIP), basic helix-loop-helix (bHLH), and APETALA2 (AP2) are central regulators of polyphyllin biosynthesis under drought conditions. Furthermore, the miRNA regulatory network showed that microRNAs (miRNAs) regulate polyphyllin biosynthesis genes either directly or via interaction with drought-responsive genes. Utilizing the Random Walk with Restart (RWR) algorithm, 98 candidate genes were prioritized, and corresponding expressed sequence tag-simple sequence repeat (EST-SSR) markers were computationally predicted. This study elucidates drought adaptation mechanisms in P. polyphylla and genetic breeding strategies for optimizing its cultivation and bioactive compound production. • Polyphyllin content of Paris polyphylla changed under different soil moisture conditions. • Drought-responsive genes in rhizomes were predominantly up-regulated under drought stress. • Basic helix-loop-helix transcription factors are potentially key regulators of polyphyllin biosynthesis under drought stress. • MicroRNAs likely influence polyphyllin production in two regulatory ways. • Random Walk with Restart algorithm identified 98 candidate genes for drought-responsive metabolite regulation.