Comparative evaluation of RAPD, ISSR and anchored-SSR markers in the assessment of genetic diversity and fingerprinting of oilseed Brassica genotypes

Forty-two genotypes representing oilseed Brassica species were analyzed for the level of genetic diversity and molecular identity using Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR) and 5'-Anchored Simple Sequence Repeat (ASSR) markers. DNA profiles revealed high degree of interspecific polymorphism, while the level was considerably low within a species, particularly in B. juncea. The UPGMA clusters clearly delineated genotypes of the respective Brassica species. Comparison of cophenetic matrices indicated a high degree of correspondence between dendrograms generated by different marker systems. A minimum of 10 random primers (approximately 105 bands) were required for the RAPD profiles to generate the expected cluster. Comparatively less number of primers was required to do the same in case of ISSR (4 primers) and ASSR (3 primers). The principal component analysis revealed similar genetic relationship among the genotypes as in cluster analysis. Although none of the DNA profiles could individually identify all the B. juncea genotypes, a combined DNA profile consisting 125 markers from the informative primers of all the three DNA marker systems could do the same.. A positive correlation was found among the marker utility parameters (calculated for individual primers of different marker systems) such as marker index (MI), resolving power (Rp) and discrimination coefficient (D) with the number of genotypes identified by each primer with a few exceptions. Single plant analysis for a set of live B. juncea varieties revealed absence of intra-varietal heterogeneity in case of ASSR profiles, thereby suggesting its utility in varietal identification and differentiation.