Evaluation of carrot genetic substructure: Comparison of the efficiency of mapped molecular markers with randomly chosen markers

In order to analyse the genetic substructure within Daucus carota, we developed several molecular markers such as microsatellites, RAPD, ISSR and AFLP markers. These markers already allow the detection of genotype clusters and the analysis of overall variability. However, fur the analysis of a large number of plant samples, as in the case of managing gene banks or for varietal identification, it seems necessary to minimise the cost and the time used for these analyses. The purpose of this research is to develop cost effective analytical procedures with minimal expense. This means procedures to obtain a maximum amount of information from a minimum amount of analysis. Based on the idea that two markers situated very close to each other, or closely linked to each other, on the genome are not as informative as two markers which are unlinked or situated far from each other, a linkage map of our markers was made by analysing 188 individuals of an F2 segregating population. The variability study was repeated by testing the markers on 13 genotypes which were considered as a representative subgroup of the morphological and geographical variability of the species such as white, yellow and orange carrots from the west of Europe and some anthocyaneous genotypes from India (purple carrots). The linkage map and the choice between markers depending on their assignation to a linkage group will be described. We compare the efficiency of using a reduced number of mapped markers with the efficiency of using more markers obtained by random choice.