Genomic variation affecting traits of adaptive significance can be considered as the prime diversity to optimize in genetic resources collections. However, which of the currently available genotyping methods is the most appropriate to estimate this variation remains an unanswered question. Ideally, information should be generated from many functional genomic regions that collectively constitute a representative sample from the total expressed DNA. Genetic diversity in a selected set of 80 Lactuca accessions was estimated using the anonymous marker systems SSR, AFLP and SSAP, and the targeted marker systems SRAP, TRAP and NBS profiling. The accessions were also described morphologically, and all characterization methods were evaluated against the genetic diversity assessed by a panel of three crop experts. The morphological data appeared weakly associated with the molecular data, and did not outperform the molecular data in relation to the expert-based assessments. In comparison with the anonymous markers, no added value was observed for the targeted markers when marker performance was related to the expert-based assessments. It could be concluded that markers that are targeted to specific gene sequences may still behave as anonymous markers if their relationship with the phenotypic variation has not been established. Furthermore, the type of marker system appeared irrelevant at low taxonomic levels if a clear genetic structure is absent, for example as a result of intensive breeding activities.
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