Effectiveness of different classes of molecular marker for classifying andrevealing variation in rice (Oryza sativa) germplasm

We have examined the effectiveness of similar numbers of markers from four molecular marker systems (AFLP, isozymes, ISSR and RAPD) for revealing gene tic diversity and discriminating between infraspecific groups of Oryza sati va germplasm. Each marker system classifies the germplasm into three major groups (most effectively with isozymes and AFLPs), but with differences (pr imarily with ISSR) between the precise classifications generated. However, at the highest levels of genetic similarity there was only partial agreemen t as to relationships between individual accessions when different markers were used. When variance was partitioned among and within the three subspec ific groups, although the differences were not significant, greater variati on was found among than within groups using AFLP and isozymes, with the rev erse for RAPD and ISSR. Measurement of polymorphism using average heterozyg osity and effective number of alleles gave similar results for each marker system. These results are discussed in relation to various genetic resource s conservation activities, and the advisability of extrapolating to other s ets of germplasm particularly of other crop species.