Integrative Biochemical and Genetic Analysis of Basil (Ocimum basilicum L.) Genotypes: Uncovering SNP Variations and Metabolic Pathway Links

Basil (Ocimum basilicum) exhibits remarkable biochemical and genetic diversity, yet the integration of genotype-specific metabolic profiles with molecular markers remains underexplored. This study characterizes three representative genotypes—Genovese, French, and Purple—using comprehensive biochemical assays, SSR and SNP markers, and multivariate analyses. Genovese basil showed the highest essential oil content (2.30%) and elevated flavonoids (rutin 40.0 μg mL⁻¹, luteolin 30.0 μg mL⁻¹), French basil accumulated caffeic (76.3 μg mL⁻¹) and benzoic acids (46.2 μg mL⁻¹), and Purple basil contained maximal apigenin (49.0 μg mL⁻¹) and hydroxycinnamic acids (coumaric 44.0 μg/mL, ferulic 23.5 μg mL⁻¹), revealing metabolic trade-offs between terpenoid and phenylpropanoid pathways. Pearson correlation and PCA confirmed coordinated regulation of metabolites and clearly separated genotypes based on biochemical specialization. SSR markers revealed 70% polymorphism, clustering French and Genovese together, while Purple formed a distinct lineage. Targeted SNP analysis identified genotype-specific nucleotide variations within amplified genomic regions, providing additional molecular signatures for genotype discrimination. The integration of biochemical traits with SNP-based clustering provides strong evidence that metabolic variation in basil is genetically structured. The identification of metabolite clusters linked to specific SNP groups offers crucial insights into the genetic basis of secondary metabolism, paving the way for enhanced breeding strategies aimed at optimizing aromatic plant traits.