Comparison of anonymous and targeted molecular markers for the estimation of genetic diversity in ex situ conserved Lactuca

Abstract

The anonymous marker systems microsatellites (simple sequence repeats), ampliWed fragment length polymorphisms and sequence-speciWc ampliWed polymorphisms were compared with the targeted marker systems sequence-related ampliWed polymorphisms, target region ampliWcation polymorphisms and nucleotide binding site proWling for their ability to describe the genetic diversity in a selected set of 80 Lactuca accessions. The accessions were also described morphologically, and all characterisation methods were evaluated against the genetic diversity assessed by a panel of three crop experts. The morphological data showed a low level of association with the molecular data, and did not display a consistently better relationship with the experts' assessments in comparison with the molecular data. In general, the diversity described by the targeted molecular markers did not diVer markedly from that of the anonymous markers, resulting in only slight diVerences in performance when related to the expert-based assessments. It was argued that markers targeted to speciWc gene sequences may still behave as anonymous markers and that the type of marker system used is irrelevant when at low taxonomic levels a clear genetic structure is absent due to intensive breeding activities. © The Author(s) 2009.