Map Resources

Physical Mapping of Peach

Contact: Albert G. Abbott, Tatyana Zhebentyayeva

Department of Genetics& Biochemistry, Clemson University, Clemson, SC, 29634, USA

Project Description

High information content fingerprinting (HICF) technique, based on capillary electrophoresis and the SNaPshot labeling kit (Luo et al., 2003. Genomics, 82(3): 378-389), is used to develop framework physical map for peach. Altogether, 16, 895 BAC fingerprints representing a 4.3x peach genome equivalent have been assembled using FPC software. The current physical map composed of 2,138 contigs containing of 15,655 BAC from both diploid Nemared and haploid Lovell libraries. According to conservative estimate, the map covers 303 Mb of the peach genome. Due to selective fingerprinting of positive BACs (~55% of BACs in database have hybridization hits), the physical map is biased to expressed euchromatic regions of genome. In total 2,636 markers (i.e. genetic markers, ESTs, cDNAs, AFLPs and overgo probes) are integrated into physical/genetic framework. The current release of the peach physical map is displayed in GDR using WebAGCoL Package.

Methods and Procedures

We employed a semi-automated CUGI fingerprinting pipeline for data processing and analysis which incorporates the use of the following software applications: ABI Data Collection v2.0, ABI GeneMapper v4.0 (software packages for ABI DNA sequencers), GenoProfiler v2.0, and FPC v8.5.3.

  • Summary of the latest peach physical map (May 2007)

    Number of clones fingerprinted
    18,141
    Number of BACs used for map contig assembly
    16,895

    Number of singletons
    Number of clones in contigs

    		1,240
    15,655

    Number of contigs

    		2,138
    Size of contigs 400-599 clones 1
    200-399 clones 4
    100-199 clones 2
    50-99 clones 2
    26-49 clones 17
    10-25 clones 356
    3-9 clones 1412
    2 clones 342
    Number of anchored contigs
    Number of assigned contigs
    		252
    87

    Physical length of the contigs
    Physical length of the anchored contigs
    Physical length of assigned contigs

    		 303Mb
    45Mb
    15.9Mb

  • Markers integrated into peach physical map (Global hybridization data)

    Hybridization probe Number of probe Genetically anchored probes
    (map name)    		 Positive BACs Average BACs
    per probe
    AFLP 17 11 (SCxB) 151 8.9
    BAC sequence
    (BAC end and BAC end overgo)    		 29  ; 121 4.2
    EST
    (unigene set of peach mesocarp ESTs)    		 2239  ; 7548 3.4
    cDNA probes 93  ; 355 3.8
    Gene specific probes 14  ; 135 9.6
    RFLP 190 127 (TxE)
    22 (FxT)
    21 (PxF)
    4 (JxF)
    		 944 5.0
    SSR 52 3 SSRs (TxE)
    21 EST-SSRs (bin map)
    8 BES-SSRs (bin map)
    10 BES-SSR (PxF)
    		 105 2.8*
    SCAR 2 1 (P2175xGN) 24 12.0
    Total 2636 228 9383 3.6
    * ‘in silico’ assigned BES-SSRs are excluded

  • View Peach Physical Map (WebFPC or WebChrom)
         View the contigs of BAC clones of peach physical map. Markers and BACs are linked to GDR sites.

  • Interactive TxE general prunus map with anchored BACs and ESTs
         Interactive map viewer that displays anchored BACs and ESTs to markers in each linkage group.

  • View/Download the Peach Transcriptome Data
         An Excel spreadsheet with peach ESTs with the anchored map positions. ESTs are anchored to genetic maps when they are hybridized to BACs that have      previously been hybridized to genetic markers. ESTs are also anchored to genetic maps when the EST-hybridizing BACs belong to a BAC contig that contains      genetically anchored BACs.


  • View/download the FPC report pages
         View and/or download FPC report pages. (for people who work on peach BAC fingerprinting).

  • Overview of the peach transcriptome map, links to download transcriptome data, and more.