Biochemical diversity across plant parts and its genetic interrelations among wild Ferula assa foetida L. populations in South Khorasan

Ferula assa‑foetida L. (Apiaceae) is a medicinally important species rich in organosulfur and terpenoid compounds, valued for its antimicrobial and digestive effects. This study investigated six wild populations from South Khorasan, Iran, to characterize organ‑specific essential oils (EOs) and assess genetic diversity. GC–MS analysis showed clear biochemical differences between aerial and underground plant parts. Foliar oils were dominated by oxygenated sesquiterpenes, especially carotol, τ‑cadinol, and 10‑epi‑γ‑eudesmol, while root and crown‑root oils were enriched in oxygenated monoterpenes and dioxanone‑type ketones such as 4,4,13‑dioxan‑2‑yl‑3,4‑dimethylcyclohex‑2‑enone. Oleo‑gum resins contained abundant sulfur‑bearing volatiles, mainly sec‑butyl disulfide and di‑isobutyl disulfide, together with mid‑chain fatty acids (dodecanoic, tetradecanoic, hexadecanoic acid). These organ‑specific chemical patterns indicate shifts in isoprenoid and sulfur‑amino‑acid metabolism under local aridity and salinity stress. ISSR markers detected high interpopulation genetic differentiation (Φ_PT = 0.516), with Koohsheib showing the greatest allelic richness and Malvand the lowest diversity. Integrated chemotypic–genetic analyses revealed strong links between genotype and environment, suggesting that ecological stressors shape secondary‑metabolite pathways. The combined molecular and phytochemical evidence offers a foundation for conservation, sustainable use, and chemovar‑based cultivation of F. assa‑foetida in arid ecosystems.