The collection of introgression lines (ILs) of Solanum lycopersicoides Dunal in the genetic background of cultivated tomato (Solanum lycopersicum L.) is a valuable tool in tomato breeding. Efficient management of the collection requires the use of molecular markers. The objective of this work was to identify polymerase chain reaction (PCR)based markers that were polymorphic between the parents of the ILs; namely 'VF36' and 'LA2951'. In total, 81 primer pairs were tested on genomic DNA from both

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... parents. Genomic DNA of the inter-specific hybrid between the two parents, from which the IL collection derives, was also tested. Markers used were either cleaved amplified polymorphic sequence (CAPS) markers or were derived from a set of conserved orthologous genes. In both cases, markers were mapped in tomato and described in the SOL Genomics Network. Forty-seven of the markers tested markers provided a single PCR product in 'VF36' and 'LA2951'. Eleven markers revealed polymorphisms as differences in band-sizes between the two parents. At least one restriction enzyme generating polymorphism was identified in 29 of the remaining 36 markers. Among other applications, some of these markers have been used to identify plants carrying the target DNA fragment among segregating generations or to delimit the length of an introgression sequence. omato (Solanum lycopersicum L.) breeding relies mainly on exploiting the variability found in wild relatives. These include a group of species native to South America, including 12 species belonging to the 'tomato clade' (i.e., Solanum section Lycopersicon) and two species each in sections Juglandifolia and