Random Amplified Polymorphic DNAs (RAPD) were used to estimate genetic distances and determine the correlation between genetic distance and hybrid performance of 29 tomato lines that were the parents in a diallel mating design. Among 97 observed bands, 69 showed polymorphism and were used for establishing genetic distances based on the Nei coefficient between parents. A UPGMA dendrogram and Multi-Dimensional Scaling (MDS) analysis based on Nei genetic distances clearly clustered each group, confirming the variation at a molecular level. Correlations between genetic distances of the parents and performances of hybrids were established for various quantitative traits. Significant correlations were found between RAPD markers estimated genetic distances and MPH, HPH, SCA for some traits. The low correlation between parental genetic distances and hybrid performances for some quantitative traits suggested that RAPD markers have low linkage to Quantitative Trait Loci (QTLs) or have inadequate genome coverage for these traits. The results indicated that RAPD markers can be used as a tool for determining the extent of genetic diversity among tomato lines, for allocating genotypes into different groups and also to aid in the choice of the superior crosses to be made among tomato lines, so reducing the number of crosses required under field evaluation.

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