title: Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Plant Genomics Institute, Chungnam National University, Daejeon, 305-764 Korea. yplim@cnu.ac.kr
authors.forename: Hyeran
authors.initials: H
authors.lastname: Kim
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.forename: Jina
authors.initials: J
authors.lastname: Bae
authors.forename: Chang Pyo
authors.initials: CP
authors.lastname: Hong
authors.forename: Seo Yeon
authors.initials: SY
authors.lastname: Lee
authors.forename: Md Jamil
authors.initials: MJ
authors.lastname: Hossain
authors.forename: Dan
authors.initials: D
authors.lastname: Van Nguyen
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.forename: Jea-Wook
authors.initials: JW
authors.lastname: Bang
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D007621:Karyotyping; D018895:Microsatellite Repeats; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D018744:DNA, Plant