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Apple, from genome to breeding

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Abstract

Genome resources for apple (Malus × domestica Borkh), the main fruit crop of temperate regions, have been developed over the past 10 years, culminating in the sequencing of the ‘Golden Delicious’ genome. The apple genome sequence anchored to a high-density linkage map provides the apple community with new tools to identify genes and other functional elements that will enable the study of the evolution of plant genome structure, as well as facilitating genomic-assisted breeding. Transcriptomics, proteomics and metabolomics studies are greatly benefiting from the availability of an annotated genome. In this review, we report on the status of the apple genome and on current molecular and genetic tools available in apple that will improve the efficiency of the process of cultivar development; we discuss how an integrative ‘omics’ approach could greatly enhance the understanding of biological processes that determine agronomically and economically favorable phenotypes; we review the databases and bioinformatics tools that are available to manage and exploit the large amounts of biological data generated for apple and other plant genomes.

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Acknowledgments

We gratefully acknowledge partial funding for PFR authors by the New Zealand Foundation for Research, Science and Technology, contract nos. CO6X0810 and C06X0812 and SNP mapping by Heather Bassett. Apple genome research and comparative genomics at FEM are supported by the research office of the Provincia autonoma di Trento.

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Author notes

  1. S. Salvi

    Present address: Department of Agroenvironmental Science and Technologies, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy

Authors and Affiliations

  1. IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E Mach 1, 38010, San Michele all’Adige, TN, Italy

    M. Troggio, S. Salvi & A. Cestaro

  2. The New Zealand Institute for Plant & Food Research Limited, Mt Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand

    A. Gleave & R. N. Crowhurst

  3. The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Manawatu Mail Centre, Palmerston North, 4442, New Zealand

    D. Chagné & S. E. Gardiner

  4. The New Zealand Institute for Plant & Food Research Limited, Hawke’s Bay, Private Bag 1401, Havelock North, 4157, New Zealand

    S. Kumar

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  1. M. Troggio
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  2. A. Gleave
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Correspondence to S. E. Gardiner.

Additional information

Communicated by A. Abbott

A contribution to the Special Issue “The genomes of the giants: a walk through the forest of tree genomes”

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Troggio, M., Gleave, A., Salvi, S. et al. Apple, from genome to breeding. Tree Genetics & Genomes 8, 509–529 (2012). https://doi.org/10.1007/s11295-012-0492-9

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