Physical Mapping of Peach
Department of Genetics & Biochemistry, Clemson University, Clemson, SC, 29634, USA
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)
Markers integrated into peach physical map (Global hybridization data)
* '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.