Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs

DNA-based fingerprinting technologies have proven useful in genetic similar ity studies. RFLP is still most commonly used in the estimation of genetic diversity in plant species, but the recently developed PCR-based marker tec hniques, RAPDs, SSRs and AFLPs, are playing an increasingly important role in these investigations. Using a set of 33 maize inbred lines we report on a comparison of techniques to evaluate their informativeness and applicabil ity for the study of genetic diversity. The four assays differed in the amo unt of polymorphism detected. The information content, measured by the expe cted heterozygosity and the average number of alleles, was higher for SSRs, while the lowest level of polymorphism was obtained with AFLPs. However, A FLPs were the most efficient marker system because of their capacity to rev eal several bands in a single amplification. In fact, the assay efficiency index was more than ten-fold higher for AFLPs compared to the other methods . Except for RAPDs, the genetic similarity trees were highly correlated. SS R and AFLP technologies can replace RFLP marker in genetic similarity studi es because of their comparable accuracy in genotyping inbred lines selected by pedigree. Bootstrap analysis revealed that, in the set of lines analyse d, the number of markers used was sufficient for a reliable estimation of g enetic similarity and for a meaningful comparison of marker technologies.