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

Abstract

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 recombinant inbred lines. This map is comprised of one morphological, 132 RFLP (restriction fragment length polymorphism, including 16 known-function genes), 33 RAPD (random amplified polymorphic DNA), and 211 AFLP (amplified fragment length polymorphism) loci. We compared the 3 types of markers for their polymorphism, segregation, and distribution over the genome. RFLP, RAPD, and AFLP methods revealed 8.7%, 15.8%, and 14.5% informative bands, respectively. This corresponded to polymorphism in 30% of RFLP probes, 32% of RAPD primers, and 100% of AFLP primer combinations. Less deviation from the 1:1 expected ratio was obtained with RFLP than with AFLP loci (8% and 18%, respectively). 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 with an average distance of 8.3 cM between markers (of the framework map). It was compared to other published interspecific maps of tomato. Despite the intraspecific origin of this map, it did not show any increase in length when compared to the high-density interspecific map of tomato.

Genetic characterization of heat tolerant tomato (Solanum lycopersicon) genotypes by SRAP and RAPD markers

“…S pimpinellifolium can be reciprocally hybridized with S. lycopersicon and it is the only species showing natural introgression with S. esculentum (Taylor, 1986). DNA markers are derived from a small region of DNA that shows sequence polymorphism between individuals within or between species and they often do not allow detection of polymorphism within the cultivated species or between the cultivated species and closely related species such as S. pimpinellifolium (Miller and Tanksley, 1990;Saliba-Colombani et al, 2000).…”

Low Genetic Diversity in the Ground Parrot (Pezoporus wallicus) Revealed by Randomly Amplified DNA Fingerprinting

“…Generally, studies which compared RAPD and AFLP (e.g. Saliba-Colombani et al 2000, Tosti & Negri 2002 found that RAPDs yield slightly higher proportion of polymorphic bands, but AFLPs are more efficient in detecting polymorphism because of the higher number of bands generated per reaction.…”

Structural analyses of the tomato genome

“…The first intraspecific map was constructed with 132 RFLP, 33 RAPD, and 211 AFLP markers using RILs derived from a cross between two inbred lines of S. lycopersicum, 'Levovil' and var. cerasiforme 'Cervil' (Saliba-Colombani et al 2000).…”