Mol Genet Genomics (2010) 283:135–145 DOI 10.1007/s00438-009-0504-0 123 ORIGINAL PAPER Genome-wide discovery of DNA polymorphism in Brassica rapa Soomin Park · Hee-Ju Yu · Jeong-Hwan Mun · Seung-Chan Lee Received: 1 September 2009 / Accepted: 2 December 2009 / Published online: 19 December 2009  Springer-Verlag 2009 Abstract Single nucleotide polymorphisms (SNPs) and/ or insertion/deletions (InDels) are frequent sequence varia- tions in the plant genome, which can be developed as molecular markers for genetic studies on crop improve- ment. The ongoing Brassica rapa genome sequencing pro- ject has generated vast amounts of sequence data useful in genetic research. Here, we report a genome-wide survey of DNA polymorphisms in the B. rapa genome based on the 557 bacterial artiWcial clone sequences of B. rapa ssp. pekinensis cv. Chiifu. We identiWed and characterized 21,311 SNPs and 6,753 InDels in the gene space of the B. rapa genome by re-sequencing 1,398 sequence-tagged sites (STSs) in eight genotypes. Comparison of our Wndings with a B. rapa genetic linkage map conWrmed that STS loci were distributed randomly over the B. rapa whole genome. In the 1.4 Mb of aligned sequences, mean nucleotide polymorphism and diversity were  = 0.00890 and  = 0.00917, respectively. Additionally, the nucleotide diversity in introns was almost three times greater than that in exons, and the frequency of observed InDel was almost 17 times higher in introns than in exons. Information regarding SNPs/InDels obtained here will provide an important resource for genetic studies and breeding pro- grams of B. rapa. Keywords Brassica rapa genome · Single-nucleotide polymorphisms · Insertion/deletions · Gene-based genetic map Introduction The Brassicaceae family includes approximately 3,700 spe- cies in 350 genera with diverse characteristics, many of which are of agronomic importance as vegetables, condi- ments, fodder, and oil crops (Beilstein et al. 2006). The genus Brassica contains the majority of Brassicaceae crop species. Of particular importance are the cole crop and veg- etable species Brassica rapa and B. oleracea, B. napus, and B. juncea as sources of canola oil, and B. nigra as mustard condiment. Because of their agricultural importance, the genomes of several Brassica crop species have been char- acterized in detail over the past few years. The genomes of three diploid species, B. rapa (AA, 2n = 20), B. nigra (BB, 2n = 16), and B. oleracea (CC, 2n = 18), have triplicated homeologous counterparts of the corresponding segments in the Arabidopsis genome due to whole-genome triplica- tion that occurred approximately 12–17 million years ago. Furthermore, an additional natural allopolyploidization event, which happened during last 10,000 years, resulted in the creation of three allotetraploid hybrids, B. juncea S. Park and H.-J. Yu contributed equally to this work. Communicated by Y. Van de Peer. Electronic supplementary material The online version of this article (doi:10.1007/s00438-009-0504-0) contains supplementary material, which is available to authorized users. S. Park · H.-J. Yu (&) · S.-C. Lee Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Suwon 441-440, Republic of Korea e-mail: yuheeju@rda.go.kr J.-H. Mun Department of Agricultural Biotechnology, National Academy of Agricultural Science, RDA, Suwon 441-707, Republic of Korea