Influence of the genetic background on the performance of molecular markers linked to seedlessness in table grapes

One of the leading goals in novel breeding programs on table grapevine is the set-up of novel seedless varieties. Seedlessness has a strong impact on consumers’ choices representing an important added economic value compared to traditional cultivars. Breeding in tree crops greatly benefits from the use of molecular markers associated to a trait of interest. Nevertheless, one of the main limitations hampering marker assisted breeding is the lack of marker validation on multiple genetic backgrounds. To this extent, we evaluated the efficiency of four markers linked to seedlessness on 97 F 1 genotypes derived from 16 cross combinations obtained through in vitro embryo rescue. Our results confirmed that the four markers were associated to seedlessness even though all, to a different extent, showed marker-trait inconsistencies. Marker efficiency was then tested on the different genetic backgrounds composing the entire germplasm providing a more acurate overview of the marker performances when the genetic background changes. Overall, the most efficient markers were VMC7f2 and p3_VvAGL11 even though their effectiveness changed remarkably from one genetic background to another. This work reports a marker validation assay on a germplasm created to encompass the actual allelic variability employed by breeders. The results could represent a valuable tool to guide the choice of the best markers to assist selection, a choice that should be based, more than on the absolute efficiency of the marker, on a careful evaluation of its performance on the genetic backgrounds in analysis.