THE COMPARISON OF RFLP, RAPD, AFLP AND SSR (MICROSATELLITE) MARKERS FOR GERMPLASM ANALYSIS

The utility of RFLP (restriction fragment length polymorphism), RAPD ( random-amplified polymorphic DNA), AFLP (amplified fragment length pol ymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information c ontent (expected heterozygosity), number of loci simultaneously analyz ed per experiment (multiplex ratio) and effectiveness in assessing rel ationships between accessions. SSR markers have the highest expected h eterozygosity (0.60), while AFLP markers have the highest effective mu ltiplex ratio (19). A single parameter, defined as the marker index, w hich is the product of expected heterozygosity and multiplex ratio, ma y be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison invol ved both cultivated (Glycine max) and wild soybean (Glycine soja) acce ssions, estimates based on RFLPs, AFLPs and SSRs are highly correlated , indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involved G. max only, then overall c orrelations between marker systems are significantly lower. Within G. max, RAPD and AFLP similarity estimates are more closely correlated th an those involving other marker systems.