Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 tropical maize inbred lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSRs). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for RAPD, for all the markers genetic distance correlated with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.