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.