Brassica species are one of the most important crop groups in terms of cultivated acreage, contribution to human and animal diets, and economic value. Of the six cultivated Brassica species, B. napus, B. rapa, B. juncea, and B. carinata provide about 12% of worldwide edible vegetable oil supplies . They also provide many of the vegetables in our daily diet such as cauliflower, broccoli, cabbage, kohlrabi, kale (B. oleracea) and turnip, Pak-choi and Chinese cabbage (B. rapa) . Brassica species are also a valuable source of dietary fiber, vitamin C and other anticancer compounds such as glucosinolates. In addition, rapeseed oil has been used as a biofuel, a desirable alternative for fossil oil worldwide.
Brassica species are closely related to the model plant Arabidopsis thaliana, and provide an opportunity to study genome rearrangements associated with polyploidization. Comparative mapping using molecular markers has already revealed extensive synteny between Brassica and Arabidopsis [3, 4]. The genomes of diploid Brassica species and Arabidopsis diverged 14.5 to 20.4 million years ago (MYA) from a common ancestor [5–7]. Subsequent chromosomal rearrangements including segmental duplications or deletions and extensive interspersed gene loss or gain events since divergence from the common ancestor have resulted in the present diploid Brassica species [6, 8], B. rapa (2n = 20, AA), B. nigra (2n = 16, BB) and B. oleracea (2n = 18, CC). The three amphidiploid species, B. juncea (2n = 36, AABB), B. napus (2n = 38, AACC), and B. carinata (2n = 34, BBCC) originated from relatively recent interspecific hybridizations among the three diploid species, most likely during human cultivation of the diploid crops . The genome relationships between these Brassica species is commonly known as the triangle of U .
The importance of Brassica species to the world economy and human health, and their potential value as models for studying genome changes associated with polyploidization, have promoted an international effort to sequence the complete set of Brassica genomes [7, 11, 12]. B. rapa ssp. pekinensis, which has the smallest genome , was selected as the representative for Brassica A genome sequencing by the Multinational Brassica Genome Project (MBGP) http://www.brassica.info, with the original aim of establishing the complete sequence of this genome using a BAC-by-BAC strategy. The BrGSP developed various genomic resources, including mapping populations, DNA libraries and DNA sequences. Three reference linkage maps, derived from the BraCKDH , BraJWF3P , and BraVCS-DH http://www.brassica-rapa.org populations, were constructed and had been served as backbones for anchoring BACs and BAC contigs for chromosome-based genome sequencing in B. rapa. Three BAC libraries covering approximately 36 genome equivalents of B. rapa were constructed using restriction enzymes Hind III, BamH I and Sau3A I. A total of 200,017 BAC-end sequences (BESs) were then generated from these BAC libraries. As of August 7, 2007, a stringent Build 2 of the physical map was released that contained 1,428 contigs with an average length of 512 kb, covering an estimated 717 Mb equivalent to 1.3 × of the B. rapa genome http://www.brassica-rapa.org. The physical map based on fingerprint analysis was integrated to the genetic map by STS and SSR markers and chromosome fluorescent in situ hybridization (FISH) analysis, which enabled the positioning of 242 gene-rich contigs to specific locations on the 10 LGs . Based on the physical map of B. rapa and the in silico comparative map of BAC-ends onto Arabidopsis chromosomes, 629 'seed' BACs spanning 86 Mb of Arabidopsis euchromatic regions were selected, distributed throughout the B. rapa genome http://www.brassica-rapa.org. These anchored BAC clones were sequenced to provide starting points ('seeds') from which to continue the whole genome sequencing http://www.brassica-rapa.org.
SSRs, or microsatellites, are tandem repeats of 1-6 nucleotide sequence motifs flanked by unique sequences . SSRs have become desirable molecular markers for gene tagging, germplasm evaluation, molecular-assisted selection and comparative mapping  because they have several advantages over other DNA markers, including being co-dominant, highly polymorphic, abundant, and distributed throughout the genome . The DNA sequence information generated from BAC-ends and anchored BACs in B. rapa by the BrGSP (e.g. http://www.brassica.bbsrc.ac.uk; http://www.brassica-rapa.org) provided an opportunity to evaluate the abundance and relative distribution of these SSRs in the whole genome [20, 21], and an excellent opportunity to develop a large number of markers with known map positions to establish direct links between genetic, physical, and sequence-based maps of the Brassica crop species.
To utilize the invaluable genomic resources developed in B. rapa for genome analysis and genetic improvement in B. napus and other cultivated Brassica species, it is necessary to integrate the genetic and physical maps to the existing B. napus genetic maps [22, 23]. The objectives of this study were to develop SSR markers from publicly available sequenced BACs in B. rapa, to integrate these markers to the existing B. napus linkage map , and to anchor these sequenced BACs and their associated BAC contigs to the A genome in B. napus. Here we report the identification and characterization of SSRs derived from sequenced BACs in B. rapa and the construction of an integrated genetic map in the A genomes of B. napus.