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Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5

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Abstract

We constructed a bacterial artificial chromosome (BAC) library, designated as KBrH, from high molecular weight genomic DNA of Brassica rapa ssp. pekinensis (Chinese cabbage). This library, which was constructed using HindIII-cleaved genomic DNA, consists of 56,592 clones with average insert size of 115 kbp. Using a partially duplicated DNA sequence of Arabidopsis, represented by 19 and 9 predicted genes on chromosome 4 and 5, respectively, and BAC clones from the KBrH library, we studied conservation and microsynteny corresponding to the Arabidopsis regions in B. rapa ssp. pekinensis. The BAC contigs assembled according to the Arabidopsis homoeologues revealed triplication and rearrangements in the Chinese cabbage. In general, collinearity of genes in the paralogous segments was maintained, but gene contents were highly variable with interstitial losses. We also used representative BAC clones, from the assembled contigs, as probes and hybridized them on mitotic (metaphase) and/or meiotic (leptotene/pachytene/metaphase I) chromosomes of Chinese cabbage using bicolor fluorescence in situ hybridization. The hybridization pattern physically identified the paralogous segments of the Arabidopsis homoeologues on B. rapa ssp. pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis.

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Acknowledgements

This research was carried out in Bio-Green project with financial support from Rural Development Administration; Korean Brassica Genome Resource Bank, Ministry of Science and Technology; and Korea Research Foundation and the Korean Federatiom of Science and Technology Societies Grant of Korea Government (MOEHRD, Basic Science Research Fund). The work at JIC was supported by the John Innes Centre Competitive Support Grant and UK Biotechnology and Biological Sciences Research Council Grant 208/IGF12449.

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Authors and Affiliations

  1. Department of Horticulture, Chungnam National University, Kung-Dong 220, Yusong-Gu, Daejeon, 305-764, South Korea

    J. Y. Park, C. P. Hong, S. J. Lee, J. W. Jeon, S. H. Lee, P. Y. Yun & Y. P. Lim

  2. Department of Biology, College of Natural Science, Chungnam National University, Kung-Dong 220, Yusong-Gu, Daejeon, 305-764, South Korea

    D. H. Koo & J. W. Bang

  3. National Institute of Agricultural Biotechnology, 250th, Seodun-dong, Gwonseon-gu Suwon Gyeonggi-do, 441-857, South Korea

    B. S. Park

  4. Arizona Genomics Institute (AGI), University of Arizona, Tucson, AZ, 85721, USA

    H. R. Kim

  5. Advanced Centre of Hill Bioresources & Biotechnology, HP Agricultural University, Palampur, 176 062, HP, India

    P. Plaha

  6. Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

    I. Bancroft

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  1. J. Y. Park
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  2. D. H. Koo
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  3. C. P. Hong
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  8. B. S. Park
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  11. P. Plaha
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  12. I. Bancroft
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  13. Y. P. Lim
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Corresponding author

Correspondence to Y. P. Lim.

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Communicated by W.R. McCombie

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Park, J.Y., Koo, D.H., Hong, C.P. et al. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Genet Genomics 274, 579–588 (2005). https://doi.org/10.1007/s00438-005-0041-4

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  • DOI: https://doi.org/10.1007/s00438-005-0041-4

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