Biochemical and Molecular Diversity in Ocimum basilicum L. Cultivars: Implications for Sustainable Germplasm Characterization and Breeding

Abstract

Basil (Ocimum basilicum) is an economically and culturally important aromatic crop whose essential oil, phenolic, and flavonoid profiles underpin its culinary, medicinal, and industrial value. Beyond flavoring, basil essential oil and leaf phenolics are applied as antifungal, insecticidal, and antibacterial agents in low-input crop protection and food preservation; therefore, the practical value of a given cultivar depends directly on which secondary metabolites it accumulates. Sustainable exploitation and conservation of basil genetic resources depend on efficient, low-input methods for linking phytochemical variation to underlying genetic markers, knowledge that remains incomplete for many commercially grown types. This exploratory study evaluated three widely cultivated basil cultivars (Genovese, French, and Purple) using biochemical assays alongside Simple Sequence Repeat (SSR) and Single-Nucleotide Polymorphism (SNP) markers, integrated through multivariate analysis, as a low-cost framework for germplasm characterization relevant to sustainable breeding pipelines. Each cultivar was represented by a single commercial seed accession, from which three biological replicates were sampled for biochemical analysis and one pooled DNA sample was used for marker analysis. The results reflect differences among three sampled accessions rather than replicated cultivar populations. Genovese basil showed the highest essential oil content and rutin/luteolin levels; French basil accumulated the most caffeic and benzoic acid; and purple basil had the highest apigenin content along with elevated coumaric and ferulic acid levels, a pattern suggestive of a possible terpenoid–phenylpropanoid trade-off warranting confirmation in replicated trials. SSR markers revealed 70% polymorphism, grouping French and Genovese together and separating purple as a distinct lineage, a pattern corroborated by 12 accession-specific SNPs in the regions examined. The concordance between biochemical and marker-based differentiation points to a genetic basis for metabolic specialization that could help prioritize cultivars for resource-efficient, marker-assisted selection, reducing the time and inputs needed to develop chemotype-targeted basil varieties. These preliminary associations should be validated in larger, independently replicated germplasm panels, but they offer a practical starting point for integrating biochemical and molecular tools into sustainable basil conservation and breeding programs.