Exploiting expressed sequence tag databases for mapping markers associated with fruit development and fruit quality in apple

Apple (Malus 9 domestica Borkh.) is one of the most important fruit trees grown in Europe and around theworld for human consumption, and therefore plant breeders aim at producing new apple varieties with high fruit quality. The availability of molecular markers suitable for marker-assisted selection could greatly increase the efficiency and power of breeding. The recent release of the cv. Golden Delicious genome sequence contributed to an exponential increase in the number of Malus sequences publicly available, while the successful achievement of two apple expressed sequence tag (EST) projects permitted the development of molecular markers from coding sequences. Here we present the setting up and mapping of new EST-based markers specific for fruit development and fruit quality traits. Since a large proportion of the ESTs used in our work were transcriptionally characterized and some of them co-localize within quantitative trait locus regions controlling fruit quality traits, the data reported will be effective in the identification of candidate genes. Due to the high level of polymorphism present in the Malus genome, 70% of the entire set of ESTs analyzed were polymorphic and 80% of them were successfully located using the conventional map-based approach. Fifty new EST-based markers were placed on the apple reference genetic map Fiesta 9 Discovery, thus enhancing the saturation of some regions, and 17 on Prima 9 Fiesta. Finally, another 17 markers were located on the Golden Delicious genome sequence using an in-silico approach.