Multi-omics reveal the molecular mechanism promoting the seed germination of Podophyllum hexandrum

Podophyllum hexandrum is an endangered medicinal plant which seeds exhibit strong dormancy, posing challenges in natural and artificial propagation due to low germination rates, long time lags, and uneven germination. Building upon previous research, we conducted an orthogonal experiment with three factors and five levels, combining cold stratification and plant growth regulator treatment, to promote the germination of P. hexandrum seeds. The results indicated that under the treatment conditions of Group 23 in the gibberellic acid treatment, the germination rate reached as high as 96.7 %, with a germination time lag of 9 days. To elucidate the molecular mechanism, we repeated these conditions and collected 10 samples at 9-day intervals starting from day 0 for transcriptome and metabolome analysis (Five experimental groups and five control groups). Through metabolome detection, a total of 59 metabolites were identified. Transcriptome analysis revealed 78,827 differential genes, closely related to the synthesis, regulation, and transduction of plant hormones at different germination stages. Combined analysis identified 23 co-expressed metabolic pathways. Weighted Gene Co-expression Network Analysis (WGCNA) identified red and yellow-green modules related to the regulation of plant hormones of interest and pinpointed hub genes: Cluster-114934.0 and Cluster-114733.0. In this systematic study, we comprehensively screened technical methods to promote the germination of P. hexandrum seeds and deeply analyzed the molecular mechanism underlying this treatment-induced germination. Our findings provide a solid theoretical foundation and technical support for the artificial propagation of P. hexandrum . • First use of melatonin to induce germination in P. hexandrum seeds. • Correlation analysis between transcriptomic and metabolomic data was performed using the WGCNA method.