Brassica is a model system for studying polyploidization and speciation since all the species in this genus have descended from a common hexaploid ancestor [1–6]. In addition, Brassica species share an ancestor with Arabidopsis, implying a similar basic genome, and thereby providing sequence-level colinearity between the two genera, particularly in euchromatic regions [7–9]. This relationship highlights the feasibility of utilizing the accumulated Arabidopsis information for the study of Brassica species. The genus Brassica includes economically important crop taxa with a wide range of morphologies, such as Chinese cabbage, mustard, cabbage, broccoli, oilseed rape, and other leafy vegetables. These taxa are classified into six genome types (AA, n = 10; BB, n = 8; CC, n = 9; AABB, n = 18; AACC, n = 19; BBCC, n = 17) according to the six representative species (AA, B. rapa; BB, B. nigra; CC, B. oleracea; AABB, B. juncea; AACC, B. napus; BBCC, B. carinata), and the genomic relationships of these taxa are well defined in U's triangle .
In view of the enomous value of Brassica in the fields of agriculture and molecular biology, genome sequencing projects have been proposed for each of the three diploid genomes . In order to better understand the A genome of Brassica and to take advantage of the colinearity between this genome and the Arabidopsis genome sequence, the multinational Brassica rapa Genome Sequencing Project (BrGSP) was launched in 2003 by scientists from five countries (Korea, Canada, the United Kingdom, China, and Australia) for sequencing B. rapa ssp. pekinensis cv. Chiifu-401-42 using a BAC-by-BAC approach . The initial objective of the BrGSP was to sequence the gene space of B. rapa, which represents approximately 330 Mb of its genome , at a Phase II quality level, whereby BACs would be sequenced to a single ordered and oriented contig, but with allowance for some gaps and ambiguous bases . The Korean group of the BrGSP [Korean Brassica Genome Project (KBGP)] sequenced 521 B. rapa BACs selected to represent genomic regions collinear with the majority of the euchromatic regions of the A. thaliana genome . These clones serve as "seed" BACs for the BrGSP, from which chromosome-scale sequencing is being initiated. The developing BrGSP has valuable resources for the community, including three BAC libraries [2, 14], 200,017 BAC end sequences , 129,928 EST sequences (by April 2008), and an initial-version reference genetic map . To date, 631 BAC sequences, representing approximately 75.3 Mb, have been made public .
The initial reference linkage map of B. rapa was constructed with 556 markers (278 AFLPs; 235 SSRs; 25 RAPDs; and a total of 18 ESTPs, STSs, and CAPSs) based on 78 doubled haploid lines (CKDH line) derived from an anther culture of the F1 of a cross between diverse Chinese cabbage (B. rapa ssp. pekinensis) inbred lines; "Chiifu-401-42" (C) and "Kenshin-402-43" (K) . Ten linkage groups, designated as A1-A10 according to the common nomenclature of the B. napus reference linkage maps , served as a reference for the BrGSP. However, there remained ambiguity in reconciling the linkage groups with the 10 B. rapa chromosomes characterized using cytogenetic approaches.
The B. rapa chromosomes have been extensively studied by karyotyping based on morphometric measurements of mitotic metaphase chromosomes [18–21]. The definitive identification of each of the individual chromosomes has been problematic because some are small-sized or similar. Recently, using fluorescence in situ hybridization (FISH), six of the 10 chromosomes were distinguished unambiguously based on the chromosomal position of repetitive sequences, such as 45S rDNA, 25S rDNA, 5S rDNA, and centromeric repeats. However, this technique can be impractical in that multiple FISHs are required to distinguish these six chromosomes, and it is unable to distinguish the remaining four chromosomes [14, 22–25]. Consequently, the BrGSP assigned each of the linkage groups (A1-A10) to the project members as chromosomal substitutes for sequencing .
In this study, we developed a second generation B. rapa reference linkage map, aligned unambiguously with the cytogenetic map of B. rapa. We also used our data to confirm and extend the comparative genome analysis of B. rapa and A. thaliana.