Abstract
In commercial apple breeding programmes, fruit quality remains the most important trait to pursue. Although many different fruit characteristics have been associated to defined genomic regions, only for a few of them markers are developed to be used in early selection. In this study, 11 molecular markers have been tested originating within or very close to genes of interest or deriving from a sequence variation of functionally analysed genes related to colour, flavour and storability. Among these, only the markers associated to red flesh, ester content, polygalacturonase activity and ethylene synthesis revealed consistent results. A collection of more than 100 commercial and old cultivars has been screened with these markers aiming at the selection of favourite candidates to be used as parents in our breeding programme. Only the old local cultivar 'Süßapfel' turned out to carry the favourable alleles for most of these quality traits. In addition, genotypic data of an aroma-related marker are correlated to chemical analyses of volatile organic compounds (VOCs) in order to verify its usefulness.