Are mapped markers more useful for assessing genetic diversity?

Genetic diversity within populations of organisms and species is commonly measured using molecular-marker data. It has been claimed that more reliable diversity measurements can be obtained using selected genetically mapped markers to ensure that all regions of the genome are represented in the data sets employed. However, this has not been tested. In the present study, using rice (Oryza sativa L.) as a model species, we have shown that the use of unmapped AFLP markers reveals a pattern of diversity that is very similar to that obtained using a range of other marker types and which reflects the known crossability groups within this species. In contrast, we show that use of mapped-marker data can, in some cases, result in highly misleading patterns of diversity: the results obtained are critically related to the choice of parents used in the cross from which the mapping population was produced. For diversity analyses, we propose that it is appropriate to use unmapped markers provided that the marker-type has been shown to have a wide distribution over the genome.