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Analyses of expressed sequence tags from apple.

Richard D Newcomb1, Ross N Crowhurst, Andrew P Gleave

  • 1Horticultural and Food Research Institute of New Zealand Limited, Mt. Albert Research Centre, Auckland, New Zealand. rnewcomb@hortresearch.co.nz

Plant Physiology
|March 15, 2006
PubMed
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Researchers generated a large collection of apple expressed sequence tags to identify genes for disease resistance and flavor compound biosynthesis. This resource aids in developing molecular markers and breeding new apple cultivars.

Area of Science:

  • Plant genomics
  • Fruit crop research
  • Molecular biology

Background:

  • The apple (Malus domestica) is a model fruit crop for studying commercially important traits.
  • Understanding apple gene function is crucial for breeding improved cultivars with enhanced disease resistance and desirable flavor profiles.

Purpose of the Study:

  • To create a comprehensive expressed sequence tag (EST) collection from apple to accelerate gene discovery.
  • To identify potential molecular markers for gene mapping and marker-assisted breeding.
  • To facilitate functional genomics research in apple.

Main Methods:

  • Generated over 150,000 expressed sequence tags from 43 cDNA libraries across 34 apple tissues and treatments.
  • Clustered sequences to obtain 42,938 nonredundant sequences, representing an estimated half of the apple transcriptome.

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  • Analyzed sequences for the abundance and distribution of molecular markers, including dinucleotide and trinucleotide repeats, and single-nucleotide polymorphisms (SNPs).

    • Main Results:

    • The EST collection represents approximately 50% of the apple's expressed genes.
    • Identified numerous potential molecular markers, with single-nucleotide polymorphisms found every 706 bp of transcribed DNA.
    • Predicted gene families involved in disease resistance and the biosynthesis of flavor and health compounds, noting potential gene duplications compared to Arabidopsis.

    Conclusions:

    • The generated apple EST resource is a valuable tool for functional genomics and genetic improvement of apple cultivars.
    • The abundance of molecular markers facilitates gene mapping and marker-assisted breeding efforts.
    • This resource will accelerate research into key apple traits, including disease resistance and the biosynthesis of valuable compounds.