Efficiency of RAPD and ISSR markers in assessment of molecular diversity in elite germplasms of Cymbopogon winterianus across West Bengal, India

Molecular characterization of eleven clones of C. winterianus collected from eleven districts of West Bengal was carried out with 10 RAPD and 9 ISSR primers. The RAPD primers developed 81 robust loci, which revealed 74.07% polymorphism and 61 ISSR markers generated 47.50% polymorphism. Out of the different anchored primer combinations, ISSR primers with AG and GA motifs produced clear and maximum scorable markers, thus revealing a better coverage of the genome. Genetic diversity parameters [average and effective number of alleles, percent polymorphism, average heterozygosity, intralocus gene diversity, polymorphic information content (PIC)] for RAPD, ISSR, and RAPD+ISSR along with UPGMA clustering based on Jaccard’s coefficient were estimated with a view to assess efficiency of the marker system in Cymbopogon. RAPD markers were more efficient than ISSR markers with regards to detection of polymorphism, number of loci scored and PIC values. However resolving power (Rp), Shannon’s index, mean coefficient of gene differentiation (Gst), and gene flow estimates were better ISSR markers. Genetic variations detected among the geographically different populations of C. winterianus 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.