Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types

Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic. In addition, a set of 9 ISSR primers were used to direct amplification of 71 PCR products, 40 (56%) of which were polymorphic. Multivariate analyses of the two PCR-based molecular marker data sets provided evidence that the patterns of variation correspond with the classification described by Glaszmann [9] using isozyme analysis. Subtle differences in the relationships revealed between rice groups using the two types of PCR-based marker led to investigations of their map positions using an intraspecific doubled haploid mapping population. The observation that the chromosomal locations of markers can influence diversity assessments is presented and the significance of this is discussed.