Research article

Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa

HyeRan Kim^{* 1,6} , Su Ryun Choi^{* 2} , Jina Bae² , Chang Pyo Hong² , Seo Yeon Lee² , Md Jamil Hossain² , Dan Van Nguyen² , Mina Jin³ , Beom-Seok Park³ , Jea-Wook Bang⁴ , Ian Bancroft⁵ and Yong Pyo Lim^1,2

¹Plant Genomics Institute, Chungnam National University, Daejeon, 305-764 Korea

²Department of Horticulture, Chungnam National University, Daejeon, 305-764 Korea

³National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, 441-707 Korea

⁴Department of Biology, Chungnam National University, Daejeon, 305-764 Korea

⁵Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

⁶Macrogen Inc., Seoul 153-023, Korea

author email corresponding author email* Contributed equally

BMC Genomics 2009, 10:432doi:10.1186/1471-2164-10-432

Published:	15 September 2009

Abstract

Background

In view of the immense value of Brassica rapa in the fields of agriculture and molecular biology, the multinational Brassica rapa Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial B. rapa linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromosomes of B. rapa. Consequently, the BrGSP assigned each of the linkage groups to the project members as chromosome substitutes for sequencing.

Results

We identified simple sequence repeat (SSR) motifs in the B. rapa genome with the sequences of seed BACs used for the BrGSP. By testing 749 amplicons containing SSR motifs, we identified polymorphisms that enabled the anchoring of 188 BACs onto the B. rapa reference linkage map consisting of 719 loci in the 10 linkage groups with an average distance of 1.6 cM between adjacent loci. The anchored BAC sequences enabled the identification of 30 blocks of conserved synteny, totaling 534.9 cM in length, between the genomes of B. rapa and Arabidopsis thaliana. Most of these were consistent with previously reported duplication and rearrangement events that differentiate these genomes. However, we were able to identify the collinear regions for seven additional previously uncharacterized sections of the A genome. Integration of the linkage map with the B. rapa cytogenetic map was accomplished by FISH with probes representing 20 BAC clones, along with probes for rDNA and centromeric repeat sequences. This integration enabled unambiguous alignment and orientation of the maps representing the 10 B. rapa chromosomes.

Conclusion

We developed a second generation reference linkage map for B. rapa, which was aligned unambiguously to the B. rapa cytogenetic map. Furthermore, using our data, we confirmed and extended the comparative genome analysis between B. rapa and A. thaliana. This work will serve as a basis for integrating the genetic, physical, and chromosome maps of the BrGSP, as well as for studies on polyploidization, speciation, and genome duplication in the genus Brassica.