COMPARISON OF AFLP AND SSR MARKERS FOR GENETIC DIVERSITY STUDIES IN MAIZE POPULATIONS

Using a set of 18 maize populations belong- ing to six different agro-ecological groups we report on a comparison of AFLP and SSR techniques to evaluate their applicability for the study of genetic diversity. Also, a DNA-pooling strategy (bulked samples) that proved to be effective in RFLP analysis of maize populations was em- ployed in order to certify if it could be applied with the same success with SSR and AFLP markers. Twenty-five SSR markers generated a total of 224 polymorphic bands, while three AFLP primer combinations generated 188 bands with 79.2% being polymorphic. The average poly- morphism content (PIC) was higher for SSRs, i.e. 0.79 for SSRs versus 0.28 for AFLPs. Higher genetic similarity (GS) values were estimated for AFLPs. The Pearson's correla- tion coefficient calculated for SSR and AFLP genetic simi- larities was low (0.149) indicating a poor agreement be- tween the two marker systems. The ranking of the agro- ecological groups according to their mean GS values (the average GS calculated for the three populations repre- senting each group) was congruent for both marker sys- tems and the Pearson's correlation coefficient calculated using these values was 0.853. The cluster analysis did not group populations precisely with expectations based up- on their agro-ecological groups, although a much better agreement was accomplished with AFLP analysis. Based on the results in this work it could be concluded that, when using a DNA-pooling strategy, AFLPs are more reli- able in assessing genetic diversity of maize populations.