Investigation of the Influence of Genetic Profile on the Economic Characteristics of Lavender Fields

Lavender (Lavandula angustifolia Mill.) is a globally significant crop, with Bulgaria maintaining a leading position in essential oil production. This study presents the first comprehensive, multi-regional analysis of commercial lavender plantations in Bulgaria, integrating phenotypic, biochemical, and genetic data. A new field quality index (FQI) was developed to evaluate production efficiency by intergating yield, essential oil quality, and intra-field homogeneity. Genetic profiling of 285 individual plants via Start-Codon-Targeted (SCoT) markers revealed significant genetic diversity and a population structure derived from two primary clusters (Delta K = 2), with high intra-field heterogeneity (64%). Our results demonstrate that peak FQI values are achieved in fields with moderate genetic diversity (genetic homogeneity index HI = 0.6–0.7) and high polymorphic information content (PIC ≥ 0.35), whereas excessive clonal uniformity compromises both yield and phytochemical complexity. The production areas in Northeastern Bulgaria (Shumen, General Toshevo, Shabla) outperformed the traditional areas (Chirpan, Kazanlak), demonstrating higher yields of high-quality essential oil. Furthermore, macroclimatic variations across the studied areas showed significant correlations with the main terpenoid components. Association analysis suggested six SCoT loci as preliminary candidates for Marker-Assisted Selection (MAS), explaining up to 33.97% of the variation in key terpenoids within this study. Furthermore the FQI is proposed as a promising conceptual framework for genome-informed management providing a strategic basis for the sustainable production of high-value lavender oil in a changing climate. The SCoT markers hold potential as useful tools for yield and quality assessment, with the possibility of inclusion in future breeding programs aimed at improving lavender production.