Newly developed SSRs based genetic diversity patterns in trait specific populations of German chamomile (Matricaria chamomilla L.)

German chamomile (Matricaria chamomilla L.) is an important essential oil bearing medicinal and aromatic plant lacking in efficient molecular markers to assist selection for its genetic improvement. In the present study, 33 novel SSR markers were developed to characterize 118 genotypes pertaining to three trait specific nurseries (erect plant type, dense biomass, higher branches) of German chamomile. A total of 670 alleles with an average of 20.30 alleles per locus were amplified over all genotypes. The average most frequent, common and rare alleles were 0.24, 13.25 and 5.13, respectively over all the loci. The high average observed heterozygosity (0.14), polymorphic information content (0.82) and genetic diversity (0.83) depicted substantial diversity among all the genotypes studied. Analysis of molecular variance revealed significant variation among populations (5%), among individuals (78%) and within individuals (17%). The unweighted neighbor joining clustering based on simple matching dissimilarity index of 33 polymorphic SSRs allocated all the genotypes in to 5 clusters. The clustering patterns observed were mostly in accordance with the trait specific populations. The principal coordinate analysis (PCoA) revealed considerable variability in all the genotypes studied and again confirmed the trait specific grouping of genotypes. A significant and positive association between genotypic and phenotypic distances was showed the efficiency of newly developed SSRs for future genetic mapping studies. The molecular data revealed high variability among the studied genotypes that may help the plant breeders to perform selections for trait specific breeding programs in German chamomile.