Full-length transcriptome and RNA-Seq analyses offer new insights into the mechanisms underlying early bolting in Peucedanum praeruptorum Dunn (Apiaceae)

Peucedanum praeruptorum Dunn, known as “Qianhu”, is a perennial herb with high value in traditional Chinese medicine. However, early bolting during cultivation significantly reduces both quality and yield, posing major challenges for its agricultural and industrial application. Our study systematically examined phenotypic traits, enzyme activity, and the levels of active ingredients. We also applied exogenous hormones to assess their effects on bolting and yield. Furthermore, we integrated second- and third-generation transcriptomic sequencing to identify genes associated with bolting. Comparative phenotypic analysis showed that both aboveground and underground parts grew more rapidly in bolting plants than in unbolting individuals. We observed increased enzyme activities such as POD and SOD, and higher MDA content in bolting plants, while CAT and APX activities decreased. A total of 452,720 ROI sequences were obtained from the PacBio platform, comprising 726,045,259 bases with an average length of 1603 base pairs. Enrichment analysis of differentially expressed genes identified two critical pathways associated with bolting: the photoperiod and vernalization pathways. Weighted gene co-expression network analysis identified seven genes associated with bolting: NAC078 , NFYC3 , VOZ1 , BRN1 , CRY2 , COL5 , and 3-MMP . Overall, this study identifies key candidate genes and co-expression networks associated with early bolting in P. praeruptorum , providing new insights into its transcriptional regulatory mechanisms. • Early bolting accelerates growth but reduces medicinal constituents in Peucedanum praeruptorum . • PP333 effectively suppresses bolting without affecting medicinal ingredient content. • Photoperiod and vernalization pathways are central to bolting regulation. • Seven bolting-associated genes ( CRY2 , COL5 , NAC078 , etc.) identified through WGCNA.