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Open Access Research article

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

Jeong-Hwan Mun1, Soo-Jin Kwon1, Tae-Jin Yang15, Hye-Sun Kim2, Beom-Soon Choi3, Seunghoon Baek1, Jung Sun Kim1, Mina Jin1, Jin A Kim1, Myung-Ho Lim1, Soo In Lee1, Ho-Il Kim1, Hyungtae Kim2, Yong Pyo Lim4 and Beom-Seok Park1*

Author Affiliations

1 Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, 225 Seodun-dong, Gwonseon-gu, Suwon 441-707, South Korea

2 Macrogen, 60-24 Gasan-dong, Geumcheon-gu, Seoul 153-023, South Korea

3 National Instrumentation Center for Environmental Management, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea

4 Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, South Korea

5 Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea

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BMC Genomics 2008, 9:280  doi:10.1186/1471-2164-9-280

Published: 12 June 2008

Abstract

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.