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The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

Cellular & Molecular Biology Letters volume 11, pages 396–407 (2006)Cite this article

Abstract

The narrow-leafed lupin possesses valuable traits for environment-friendly agriculture and for the production of unconventional agricultural products. Despite various genetic and environmental studies, the breeding of improved cultivars has been slow due to the limited knowledge of its genomic structure. Further advances in genomics require, among other things, the availability of a genomic DNA library with large inserts. We report here on the construction of the first DNA library cloned in a BAC (bacterial artificial chromosome) vector from diploid Lupinus angustifolius L. cv. Sonet. The high molecular weight DNA used for its preparation was isolated from interphase nuclei that were purified by flow cytometry. The library comprises 55,296 clones and is ordered in 144×384-well microtitre plates. With an average insert size of 100 kb, the library represents six haploid genome equivalents. Thanks to the purification of the nuclei by flow cytometry, contamination with chloroplast DNA and mitochondrial DNA was negligible. The availability of a BAC library opens avenues for the development of a physical contig map and positional gene cloning, as well as for the analysis of the plant’s genome structure and evolution.

Abbreviations

BAC:

bacterial artificial chromosome

DAPI:

4′,6-diamidino-2-phenylindole

FISH:

fluorescence in situ hybridization

HMW:

high molecular weight

PAC:

artificial bacteriophage P1 chromosome

PFGE:

pulsed field gel electrophoresis

PRINS:

primed in situ DNA labeling

YAC:

yeast artificial chromosome

References

  1. Gladstones, J.S. Lupins of the Mediterranean region and Africa. Technical Bull. 26, Dept. of Agriculture Western Australia, 1974.

  2. López-Bellido, L., Fuentes, M., Lhamby, J.C.B. and Castillo, J.E. Growth and yield of white lupin (L. albus) under Mediterranean conditions: effect of sowing date. Field Crops Res. 36 (1994) 87–94.

    Article  Google Scholar 

  3. Edwards, A.C. and van Barneveld, R.J. Lupins for livestock and fish. In: Lupins as Crop Plants: Biology, Production and Utilisation. (Gladstones, J.S., Atkins, C. and Hamblin, J., Eds) CAB International, London, 1998, 385–411.

    Google Scholar 

  4. Bhardwaj, H.L. Evaluation of lupin as a new food/feed crop in the Mid-Atlantic region. In: Trends In New Crops and New Uses (Janick, J. and Whipkey, A., Eds) ASHS Press, Aleksandria, 2002, 115–119.

    Google Scholar 

  5. Herridge, D.F. and Doyle, A.D. The narrow-leafed lupin (Lupinus angustifolius L.) as a nitrogen-fixing rotation crop for cereal production. II Estimates of fixation by field-grown crops. Austr. J. Agri. Res. 39 (1988) 1017–1028.

    Article  Google Scholar 

  6. Petterson, D.S. and Harris, D.J. Cadmium and lead content of lupin seed grown in Western Australia. Austr. J. Exp. Agric. 35 (1995) 403–407.

    Article  CAS  Google Scholar 

  7. Wink, M., Meißner, C. and Witte, L. Patterns of quinolizidine alkaloids in 56 species of the genus Lupinus. Phytochemistry 38 (1995) 139–153.

    Article  CAS  Google Scholar 

  8. Kachlicki, P., Marczak, ł., Kerhoas, L., Einhorn, J. and Stobiecki, M. Profiling isoflavone conjugates in root extracts of lupine species with LC/ESI/MSn systems. J. Mass Spectrom. 40 (2005) 1088–1103.

    Article  PubMed  CAS  Google Scholar 

  9. Wink, M. Chemical defence of Lupinus. Mollusc-repellent properties of quinolizinidine alkaloids. Z. Naturforsch. 39c (1993) 553–558.

    Google Scholar 

  10. Folkman, W., Szrechan, J. and Gulewicz, K. Preparations of alkaloid-rich lupin in plant protection: an effect of the preparations on feeding and development of Piersi brassicaceae L. and Piersi rapae L. J. Plant Prot. Res. 42 (2002) 143–155.

    CAS  Google Scholar 

  11. Wolko, B. and Weeden, N.F. Linkage map of isozymes and RAPD markers for L. angustifolius L. Proceedings of the VIIth International Lupin Conference, Evora, Portugal, 1993, 42–49.

    Google Scholar 

  12. Kruszka, K. and Wolko, B. Linkage maps of morphological and molecular markers in lupins. Proceedings of the 9 th International Lupin Conference, An Ancient Crop for the New Millenium. (van Santen, E., Wink, M., Weissmann, S. and Roemer, P. Eds) Klink/Müritz, Germany, 1999, 100–110.

    Google Scholar 

  13. Boersma J.G., Pallotta, M., Li, C., Buirchell B.J., Sivasithamparam K. and Yang, H. Construction of a genetic linkage map using MFLP, and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus angustifolius). Cell. Mol. Biol. Lett. 10 (2005) 331–344.

    PubMed  CAS  Google Scholar 

  14. You, M., Boersma, J.G., Buirchell, B.J., Sweetingham, M.W., Siddique, K.H.M. and Yang, H. A PCR-based molecular marker applicable for marker-assisted selection for anthracnose disease resistance in lupin breeding. Cell. Mol. Biol. Lett. 10 (2005) 123–134.

    PubMed  CAS  Google Scholar 

  15. Pazy, B., Heyn, C.C., Hermstadt, I. and Plitmann, U. Studies in populations of the Old World Lupinus species. Chromosomes of the East-Mediterranean lupines. Israel J. Bot. 26 (1977) 115–127.

    Google Scholar 

  16. Carstairs, S.A., Buirchell, B.J. and Cowling, W.A. Chromosome number, size and interspecific crossing ability of three Old World lupins, Lupinus princei Harms, L. atlanticus Gladstones and L. digitatus Forskal, and implications for cyto-systematic relationships among the rough-seeded lupins. J. R. Soc. West. Aust. 75 (1992) 83–88.

    Google Scholar 

  17. Naganowska, B. and Zielińska A. Physical mapping of 18S–25S rDNA and 5S rDNA in Lupinus by fluorescent in situ hybridization. Cell. Mol. Biol. Lett. 7 (2002) 665–670.

    PubMed  CAS  Google Scholar 

  18. Naganowska, B., Doležel J. and Święcicki, W.K. Development of molecular cytogenetics and physical mapping of ribosomal RNA genes in Lupinus. Biol. Plant. 46 (2003) 211–215.

    Article  CAS  Google Scholar 

  19. Hajdera, I., Siwińska, D., Hasterok, R. and Małuszyńska, J. Molecular cytogenetic analysis of genome structure in Lupinus angustifolius and Lupinus cosentinii. Theor. Appl. Genet. 107 (2003) 988–996.

    Article  PubMed  CAS  Google Scholar 

  20. Naganowska, B. and Kaczmarek, A. Repetitive DNA sequences in cytogenetic studies of the Lupinus genome. In: Mexico, Where Old and New World Lupins Meet. Proceedings of the 11th International Lupin Conference (van Santen, E. and Hill, G.D. Eds), Guadalajara, Jalisco, Mexico. May 4–9, 2005. International Lupin Association, Canterbury, New Zealand, ISBN 0-86476-165-1 (2005) 27–29.

    Google Scholar 

  21. Obermayer, R., Święcicki, W.K. and Greilhuber, J. Flow Cytometric Determination of Genome Size in some Old World Lupinus Species (Fabaceae). Plant Biol. 1 (1999) 403–407.

    Google Scholar 

  22. Naganowska, B., Wolko, B., Śliwińska, E. and Kaczmarek, Z. Nuclear DNA Content Variation and Species Relationships in the Genus Lupinus (Fabaceae). Ann. Bot. 92 (2003) 349–355.

    Article  PubMed  CAS  Google Scholar 

  23. Primrose, S.B. Principles of Genome Analysis. A guide to Mapping and Sequencing DNA from Different Organisms. Blackwell Sciences Ltd Second Edition, 1998, 54–60.

  24. Zhang, H.B., Woo, S.S. and Wing, R.A. BAC, YAC and cosmid library construction. in: Plant Gene Isolation. Principles and Practice (Foster G.D. and Twell, D. Eds.), John Wiley and Sons Ltd., 1996, 75–99.

  25. Peterson, D.G., Tompkins, J.P., Wing, R.A. and Paterson A.H. Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. J. Agric. Genom. 5 (2000) 1–100.

    Google Scholar 

  26. Choi, S., Creelman, R.A., Mullet, J.E. and Wing, R.A. Construction and characterization of bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol. Biol. Rep. 13 (1995) 124–128.

    Google Scholar 

  27. Yang, D., Parco, A., Nandi, S., Subudhi, P., Zhu, Y., Wang, G. and Huang, N. Construction of a bacterial artificial chromosome (BAC) library and identification of overlapping BAC clones with chromosome 4-specific RFLP markers in rice. Theor. Appl. Genet. 95 (1997) 1147–1154.

    Article  CAS  Google Scholar 

  28. Nam, Y.W., Penmesta, R. V., Endre, G., Uribe, P., Kim, D. and Cook, D.R. Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes. Theor. Appl. Genet. 98 (1999) 638–646.

    Article  CAS  Google Scholar 

  29. Lijavetzky, D., Muzzi, G., Wicker, T., Keller, B., Wing, R. and Dubcovsky, J. Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42 (1999) 1176–1182.

    Article  PubMed  CAS  Google Scholar 

  30. Allouis, S., Moore, G., Bellec, A., Sharp, R., Faivre, P., Montimer, K., Pateyron, S., Foote, T., Griffiths, S., Caboche, M. and Chalhoub, B. Construction and characterisation of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm “Chinese Spring”. Cereal. Res. Comm. 31 (2003) 331–338.

    CAS  Google Scholar 

  31. Tomkins, J.P., Frisch, D.A., Byrum, J.R., Jenkins, M.R., Barnett, L.J., Wicker, T., Luo, M. and Wing, R.A. Construction and characterization of a maize bacterial artificial chromosome (BAC) library for the inbred line LH132. Maize Genet. Coop. News Lett. (2000) 74 www.agron.missouri.edu/mnl/74.

  32. Yu, Y., Tomkins, J.P., Waugh, R., Frisch, D.A., Kudrna, D., Kleinhofs, A., Brueggeman, R.S., Muehlbauer, G.J., Wise, R.P. and Wing, R.A. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor. Appl. Genet. 101 (2000) 1093–1099.

    Article  CAS  Google Scholar 

  33. Danesh, D., Peňula, S., Mudge, J., Denny, R.L., Nordstrom, H., Martinez, J.P. and Young, N.D. A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor. Appl. Genet. 96 (1998) 196–202.

    Article  CAS  Google Scholar 

  34. Song, J., Dong, F. and Jiang, J. Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetic research. Genome 43 (2000) 199–204.

    Article  PubMed  CAS  Google Scholar 

  35. Vanhouten, W. and MacKenzie, S. Construction and characterization of a common bean bacterial artificial chromosome library. Plant Mol. Biol. 40 (1999) 977–983.

    Article  PubMed  CAS  Google Scholar 

  36. Folkertsma, R.T., Spassova, M. I., Prins, M., Stevens, M.R., Hille, J. and Goldbach, R.W. Construction of a bacterial artificial library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus. Mol. Breed. 5 (1999) 197–207.

    Article  CAS  Google Scholar 

  37. Doležel, J., Číhalíková, J. and Lucretti, S. A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L. Planta 188 (1992) 93–98.

    Article  Google Scholar 

  38. Doležel, J., Číhalíková, J., Weiserowa, J. and Lucretti, S. Cell cycle synchronization in plant root meristems. Methods Cell Sci. 21 (1999) 95–107.

    Article  PubMed  Google Scholar 

  39. Šimková, H., Číhalíková, J., Vrána, J., Lysák, M.A. and Doležel, J. Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol. Plant. 46 (2003) 369–373.

    Article  Google Scholar 

  40. Šafář, J., Noa-Carrazana, J.C., Vrána, J., Bartoš, J., Alkhimova, O., Lheureux, F., Šimková, H., Caruana, M.L., Doležel, J. and Piffanelli, P. Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome. Genome 47 (2004) 1182–1191.

    Article  PubMed  Google Scholar 

  41. Woo, S.S., Jiang, J., Gill, B.S., Paterson, A.H., and Wing, R.A. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res. 22 (1994) 4922–4931.

    PubMed  CAS  Google Scholar 

  42. Sambrook, J. and Russell, D.W. Molecular Cloning. A Laboratory Manual. Third Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA vol. 3 (2001) A 2.4.

    Google Scholar 

  43. Yang, H., McLeese, J., Weisbart, M., Dionne, J.-L. and Aubin R.A. Simplified high throughput protocol for Northern hybridization. Nucleic Acids Res. 21 (1993) 3337–3338.

    PubMed  CAS  Google Scholar 

  44. Doležel, J., Bartoš, J., Voglmayr, H. and Greilhuber, J. Nuclear DNA content and genome size of trout and human. Cytometry 51 (2003) 127–128.

    Article  PubMed  Google Scholar 

  45. Clarke, L. and Carbon, J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 9 (1976) 91–99.

    Article  PubMed  CAS  Google Scholar 

  46. Wolko, B., Kasprzak, A., Doležel, J. and Naganowska, B. Screening a Narrow-Leafed Lupin BAC Library to Search for Clones Containing Nodulation and Disease Resistance Genes. Proc. of the 11 th International Lupin Conference: Mexico, Where Old and New World Lupins Meet. Guadalajara, Mexico, 2005, 49–51.

    Google Scholar 

  47. Mozo, T., Dewar, K., Dunn, P., Ecker, J.R., Fischer, S., Kloska, S., Lehrach, H., Marra, M., Martienssen, R., Meier-Ewert, S. and Altmann, T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat. Genet. 22 (1999) 271–275.

    Article  PubMed  CAS  Google Scholar 

  48. Islam-Faridi, M.N., Childs, K.L., Klein, P.E., Hodnett, G., Menz, M.A., Klein, R.R., Rooney, W.L., Mullet, J.E., Stelly, D.M. and Price, H.J. A molecular cytogenetic map of sorghum chromosome 1: fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes. Genetics 161 (2002) 345–353.

    PubMed  CAS  Google Scholar 

  49. Suzuki, G., Ura, A., Saito, N., Do, G.S., Yamamoto, M., Mukai, Y. and Seo, B.B. BAC FISH analysis in Allium cepa. Genes Genet. Syst. 76 (2001) 251–255.

    Article  PubMed  CAS  Google Scholar 

  50. Zhang, P., Li, W., Fellers, J., Friebe, B. and Gill, B.S. BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112 (2004) 288–299.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland

    Andrzej Kasprzak, Bogdan Wolko & Barbara Naganowska

  2. Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Sokolovská 6, CZ-772 00, Olomouc, Czech Republic

    Jan Šafář, Jaroslav Janda & Jaroslav Doležel

Authors
  1. Andrzej Kasprzak
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  2. Jan Šafář
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  3. Jaroslav Janda
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  4. Jaroslav Doležel
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  5. Bogdan Wolko
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  6. Barbara Naganowska
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Correspondence to Bogdan Wolko.

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Kasprzak, A., Šafář, J., Janda, J. et al. The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.). Cell Mol Biol Lett 11, 396–407 (2006). https://doi.org/10.2478/s11658-006-0033-3

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  • DOI: https://doi.org/10.2478/s11658-006-0033-3

Key words

  • BAC
  • Genomic DNA library
  • Lupinus angustifolius
  • Narrow-leafed lupin

Cellular & Molecular Biology Letters

ISSN: 1689-1392

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