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


CONCLUSIONS
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.
Mun
Jeong-Hwan
JH
Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, 225 Seodun-dong, Gwonseon-gu, Suwon 441-707, South Korea. munjh@rda.go.kr
Kwon
Soo-Jin
SJ
Yang
Tae-Jin
TJ
Kim
Hye-Sun
HS
Choi
Beom-Soon
BS
Baek
Seunghoon
S
Kim
Jung Sun
JS
Jin
Mina
M
Kim
Jin A
JA
Lim
Myung-Ho
MH
Lee
Soo In
SI
Kim
Ho-Il
HI
Kim
Hyungtae
H
Lim
Yong Pyo
YP
Park
Beom-Seok
BS
D029741:Brassica rapa / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D020451:Contig Mapping; D016172:DNA Fingerprinting; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D015698:Genomic Library; D023281:Genomics; D020161:Physical Chromosome Mapping; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D016324:Sequence Tagged Sites
D005819:Genetic Markers