Microsatellite markers’ based molecular divergence among the breeding lines of aromatic marigold (Tagetes minuta L.)

Aromatic marigold (Tagetes minuta L.) is an essential oil-bearing plant of industrial value. The essential oil obtained from the plant has high demand in the flavor and perfume industry. The present study investigates the molecular diversity patterns using microsatellite markers in 126 breeding lines representing three groups (higher, intermediate, and lower biomass) based on phenotypic characterization. These lines are being maintained through repeated selfing. A total of 503 alleles with an average of 16.23 alleles per locus were detected at 31 SSR loci over all the genotypes. The average most common and rare alleles were 3.35 and 12.87, respectively, over all the studied loci. The high polymorphic information content (0.88) and genetic diversity (0.89) indicate high allelic diversity among the genotypes studied. Ten genotype-specific markers were identified. Significant molecular variances have been observed among the groups (3 %), among individuals (72 %), and within individuals (26 %). The unweighted neighbor-joining clustering based on a simple matching dissimilarity index grouped all 126 genotypes into five major clusters. The clustering pattern primarily follows the biomass-specific distribution of populations. The principle coordinate analysis depicts considerable variations and again confirms the biomass-specific grouping of genotypes. The highly significant positive association between genotypic and phenotypic distances indicates the importance of these marker loci for future marker-assisted selection and association mapping studies.