Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L.

The aim of this study was to develop a cultivar identification tool based on molecular analysis and a statistical approach. From the PIC parameter we defined the D parameter, which evaluates the efficiency of a primer for the purpose of identification of varieties; i.e. the probability that two randomly chosen individuals have different patterns. D can be used to compare different types of markers even if only the allelic frequencies are known. We used this parameter to develop an algorithm for selecting the optimal combination of primers necessary to identify a set of varieties. The optimal combination of primers determined for a small elite group of varieties applied on a larger set induces a risk of confusion involving 1 of the elite varieties. We estimated the risk of confusion using the D value of each primer of the combination. We applied this methodology on a set of 224 varieties of Vitis vinifera screened with 21 RAPD primers and two microsatellite loci. The discriminating power of the primers did not only depend on the number of patterns it generates but also on the frequencies of the different patterns. A combination of 8 primers (6 RAPD and two microsatellite) was found to be optimum for the discrimination of these 224 varieties. A subset of 38 elite varieties was also investigated. The determined optimal combination of 4 primers (3 RAPD and one microsatellite) applied on the 224 varieties gave 9 risks of confusion involving 1 of the elite varieties. Confusion can happen between varieties with the same origin as well as between varieties of very diverse geographical origins.