Efficiency of ISSR marker for characterization of Cymbopogon germplasms and their suitability in molecular barcoding

Abstract

The genus Cymbopogon possesses a large number of odoriferous species of the grass family (Poaceae) and is characterized by plants bearing aromatic essential oils in all parts. In the present study, ten Indian elite cultivars of Cymbopogon aromatic grasses of essential oil trade types of Citronella, Palmarosa and Lemongrass were characterized by means of inter-simple sequence repeats (ISSRs) to discern the extent of genetic variation and to develop a fingerprinting key. Fifteen ISSR primers were screened, and 12 primers were selected based on their repeatability, scorability and their ability to distinguish between cultivars. Out of the 77 loci scored, 67 were found to be polymorphic with an average of 5.58 polymorphic loci per primer. Primary allelic variability and the genetic bases of the cultivated germplasm were computed through parameters of percentage of polymorphic loci, observed number of alleles, effective number of alleles, Nei’s gene diversity, and Shannon’s information indices. The allelic diversity was found to be in the order: Palmarosa > Lemongrass > Citronella. Polymorphism differed substantially within the discrete groups of cultivars and was approximately 81.81 % in Palmarosa, 5.19 % in Citronella and 36.36 % in Lemongrasses. Discriminating power of ISSR markers was assessed by calculating polymorphic information content, effective multiplex ratio, marker index and resolving power. The primers that showed higher polymorphism had higher EMR and MI values. Also, ISSRs of diagnostic and curatorial importance were discerned as ‘stand alone’ molecular descriptors for barcoding the application of DNA sequences of standardized genetic markers for the identification of eukaryotic organisms. The order of the average value of Jaccard’s coefficient of similarity was found to be Citronella (0.915) > Lemongrass (0.611) > Palmarosa (0.472). An incongruity was observed between the positions of cultivars in the cluster and also revealed from the principal coordinate analysis. The present study could be of much use for the introgression of new characters from wild counterparts to the cultivars, isolation of stable segregating markers, and selection of improved varieties and conservation of germplasm resources.