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Background  The genus  Brassica  includes the most extensively cultivated vegetable crops worldwide. Investigation of the  Brassica  genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the  B. rapa  genome is a fundamental tool for analysis of  Brassica  "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences.    Results  A genome-wide physical map of the  B. rapa  genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing.    Conclusion  The map reported here is the first physical map for  Brassica  "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between  Brassica  genomes. The current build of the  B. rapa  physical map is available at the  B. rapa  Genome Project website for the user community.

The first generation of a BAC-based physical map of Brassica rapa