Molecular Breeding

, Volume 29, Issue 3, pp 699–715 | Cite as

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

  • Valentina Cova
  • Davide Perini
  • Valeria Soglio
  • Matteo Komjanc
  • Eric van de Weg
  • Cesare Gessler
  • Luca Gianfranceschi


Apple (Malus × domestica Borkh.) is one of the most important fruit trees grown in Europe and around the world 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 × Discovery, thus enhancing the saturation of some regions, and 17 on Prima × Fiesta. Finally, another 17 markers were located on the Golden Delicious genome sequence using an in-silico approach.


Candidate genes ESTs Fruit development Functional molecular markers Malus × domestica Mapping 



This work was carried out in the context of HiDRAS (High-Quality Disease Resistant Apples for a Sustainable Agriculture) Project, with the financial support from the Commission of the European Communities (Contract No. QLK5-CT-2002-01492), Directorate General Research—Quality of Life and Management of Living Resources Program. This manuscript does not necessarily reflect the Commission’s views and in no way anticipates its future policy in this area. The authors thank Andrea Patocchi, Agroscope Wädenswil, Switzerland,for providing the mapping data of Fiesta × Discovery population.

Supplementary material

11032_2011_9584_MOESM1_ESM.doc (178 kb)
Supplementary material 1 (DOC 179 kb)


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Valentina Cova
    • 1
  • Davide Perini
    • 2
  • Valeria Soglio
    • 2
  • Matteo Komjanc
    • 1
  • Eric van de Weg
    • 3
  • Cesare Gessler
    • 4
  • Luca Gianfranceschi
    • 2
  1. 1.IASMA Research and Innovation CentreFondazione Edmund MachS. Michele all’AdigeItaly
  2. 2.Dipartimento di Scienze Biomolecolari e BiotecnologieUniversità degli Studi di MilanoMilanItaly
  3. 3.Plant BreedingWageningen University and Research CentreWageningenThe Netherlands
  4. 4.Plant PathologyInstitute of Integrative Biology (IBZ)ZurichSwitzerland

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