Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome

We have constructed a tomato genetic linkage map based on an intraspecific cross between two inbred lines of Lycopersicon esculentum and L. esculentum var. cerasiforme. The segregating population was composed of 153 recombina nt inbred lines. This map is comprised of one morphological, 132 RFLP (rest riction fragment length polymorphism, including 16 known-function genes), 3 3 RAPD (random amplified polymorphic DNA), and 211 AFLP (amplified fragment length polymorphism) loci. We compared the 3 types of markers for their po lymorphism, segregation, and distribution over the genome. RFLP, RAPD, and AFLP methods revealed 8.7%, 15.8%, and 14.5% informative bands, respectivel y. This corresponded to polymorphism in 30% of RFLP probes, 32% of RAPD pri mers, and 100% of AFLP primer combinations. Less deviation from the 1:1 exp ected ratio was obtained with RFLP than with AFLP loci (8% and 18%, respect ively). RAPD and AFLP markers were not randomly distributed over the genome . Most of them (60% and 80%, respectively) were grouped in clusters located around putative centromeric regions. This intraspecific map spans 965 cM w ith an average distance of 8.3 cM between markers (of the framework map). I t was compared to other published interspecific maps of tomato. Despite the intraspecific origin of this map, it did not show any increase in length w hen compared to the high-density interspecific map of tomato.