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 novel Field Quality Index (FQI) was developed to objectively quantify production efficiency by balancing 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. Regions in Northeastern Bulgaria (Shumen, Shabla) outperformed traditional areas, showing superior resilience to heat stress, which was found to suppress linalool biosynthesis while stimulating trans-ocimene accumulation. Association analysis identified six SCoT loci with high potential for Marker-Assisted Selection (MAS), explaining up to 33.97% of the variation in key terpenoids. These findings establish the FQI as a robust tool for genome-informed management and provide a strategic framework for the sustainable production of high-value lavender oil in a changing climate. The SCoT markers demonstrate substantial potential for practical use in assessing yield and quality, as well as for integration into breeding programs aimed at advancing lavender production.