Peucedanum praeruptorum is increasingly cultivated as wild resources are depleted. However, cultivated plants often contain lower levels of coumarins than wild individuals and may not meet the standards of the Chinese Pharmacopoeia. To clarify whether growth year could influence coumarin accumulation, we analyzed P. praeruptorum populations cultivated for 1–3 years using a newly developed 17-coumarin quantification method and conducted transcriptomics to characterize gene expression across growth years. The results suggest that total coumarins and major pyranocoumarins (notably praeruptorin B) increased steadily with growth years, while furanocoumarins and simple coumarins increased initially then declined. Notably, despite substantial intra-population variation in coumarin content, cultivated plants could be classified into two distinct chemotypes: chemotype A (higher praeruptorin A and praeruptorin E, lower praeruptorin B) and chemotype B (lower praeruptorin A and praeruptorin E, higher praeruptorin B, pteryxin, and qianhucoumarin D than chemotype A). Both chemotypes coexisted across all examined populations, with the proportion of chemotype B increasing with growth years. Transcriptomic profiling revealed that 3-year-old plants showed higher expression of pyranocoumarin biosynthetic genes and lower expression of genes associated with simple coumarin and furanocoumarin biosynthesis compared with 1-year-old plants. Differential expression analysis further identified key candidate genes associated with growth years and chemotypes. Together, these results demonstrate that growth year and chemotype synergistically regulate coumarin accumulation in cultivated P. praeruptorum, providing a two-dimensional framework for improving the quality of cultivated medicinal materials.

Perilla frutescens(L.) Britt. (P. frutescens) is an important medicinal and aromatic plant, whose leaf color and chemotype strongly influence its medicinal quality and economic value. All the previously discovered perillene (PL)-type P. frutescens are double-sided green, and whether the PL-type trait is tightly linked with the green-leaf trait in genetics remains to be clarified. This study aimed to address this question and attempt to create purple-leaf PL-type germplasm through perillaldehyde (PA) × PL hybridization. Three parallel experiments were conducted using purple-leaf PA-type P. frutescens as male parents and green-leaf PL-type P. frutescens as female parents. Chemotypes were identified by gas chromatography (GC). Association analyses between leaf color and chemotype were performed in segregating F₂ populations. Genes involved in leaf color formation and PL biosynthesis were mapped onto the published Hoko-3 reference genome to provide genomic evidence for the genetic relationship between the two traits. All F₁ individuals were uniformly PA-type. The three F₂ populations exhibited distinct leaf color–chemotype association patterns: Z01 (n = 118) showed a strong association (Fisher’s exact p = 9.13 × 10⁻¹⁰; φ = 0.564), Z02 (n = 117) showed no detectable association (p = 0.9; φ = 0.012), and Z03 (n = 88) showed a moderate association (p = 0.00669; φ = 0.289). Importantly, purple-leaf PL-type recombinants were obtained in F₂ populations and stably maintained through subsequent generations (F₃–F₅), demonstrating that the PL-type trait is not tightly linked with the green-leaf trait in P. frutescens. Genomic mapping genes related to leaf color and PL biosynthesis are distributed across multiple chromosomes and usually present as multiple loci, which is consistent with the pattern of incomplete linkage. The PL-type trait is recessive and not genetically tightly linked to the green-leaf traits in P. frutescens. The successful creation of a purple-leaf PL-type germplasm breaks the historical phenotypic constraint and provides a novel material for further dissection of the molecular mechanisms regulating secondary metabolism and organ coloration in P. frutescens.