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Genome-wide discovery of DNA polymorphism in Brassica rapa

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Abstract

Single nucleotide polymorphisms (SNPs) and/or insertion/deletions (InDels) are frequent sequence variations in the plant genome, which can be developed as molecular markers for genetic studies on crop improvement. The ongoing Brassica rapa genome sequencing project 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 artificial clone sequences of B. rapa ssp. pekinensis cv. Chiifu. We identified 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 findings with a B. rapa genetic linkage map confirmed 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 θ = 0.00890 and π = 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 programs of B. rapa.

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Acknowledgments

We thank Dr. Ik-Young Choi of NICEM, Dr. Venkatesan Sundaresan of UC Davis, and Dr. Dae-Geun Oh of KNCAF for helpful comments on this paper. We also thank Man-Ki Kim of NIHHS, MACROGEN Co., and NICEM for technical assistance, Beom-Seok Park of NAAS for genetic mapping information, and Dr. Soo-Seong Lee of BBI, Dr. Yong Pyo Lim of CNU, and Dr. Su Hyoung Park of NIHHS for providing plant materials. This work was supported by NIHHS grants 2007139057600000502 and 200901FHT020508395, and by Post Doctoral Course Program of NIHHS for Soomin Park, Rural Development Administration, Republic of Korea.

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  1. Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Suwon, 441-440, Republic of Korea

    Soomin Park, Hee-Ju Yu & Seung-Chan Lee

  2. Department of Agricultural Biotechnology, National Academy of Agricultural Science, RDA, Suwon, 441-707, Republic of Korea

    Jeong-Hwan Mun

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  1. Soomin Park
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Correspondence to Hee-Ju Yu.

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Communicated by Y. Van de Peer.

S. Park and H.-J. Yu contributed equally to this work.

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438_2009_504_MOESM1_ESM.xls

Summary of DNA polymorphisms discovered in this study with a list of source BAC accessions used for this polymorphism survey (XLS 9078 kb)

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Park, S., Yu, HJ., Mun, JH. et al. Genome-wide discovery of DNA polymorphism in Brassica rapa . Mol Genet Genomics 283, 135–145 (2010). https://doi.org/10.1007/s00438-009-0504-0

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