Test of equivalence of PCR-based marker systems in assessing genetic variability and molecular characterization of Jatropha curcus: A case study

PCR-based molecular markers, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR) and Simple Sequence Repeat (SSR) used for genetic characterization in Jatropha revealed 100, 98.68 and 97.47 per cent polymorphism, respectively.The highest genetic correlation according to combined RAPD, ISSR, and SSR data was between genotypes PKVJ-DHW-1 and P.J.-03004 (83.7%), while the lowest similarity was found between genotypes TNMC-2 and TNMC-4.The dendrogram of combined RAPD, ISSR and SSR data grouped genotypes into nine major clusters. Each marker grouped TNMC-2 into unique cluster. Cophenetic correlation (r) for RAPD, ISSR, SSR and their combination were 0.9873, 0.9840, 0.7769 and 0.9886, respectively, indicating very good fit of the cluster analysis and showed significant correlation between similarity matrix and cluster analysis.The PCoA for RAPD, ISSR, SSR and combined markers also resulted in similar relationship between the score plots and the pattern of genetic diversity estimated by the UPGMA cluster analysis. Results clearly indicated that the combination of ISSR vs. SSR (r = 0.4835) would be more effective for genetic diversity analysis than other combinations.Thus, bulk analyses of RAPD, ISSR and SSR-PCR markers provides a quick, reliable and highly informative system for DNA fingerprinting in Jatropha and also permit to establish genetic relationships which agree with, by other means, known origin of the Jatropha cultivars.