Skip to main content
SpringerLink
Log in
Book cover

Plant Cytogenetics pp 135–149Cite as

Construction of BAC Libraries from Flow-Sorted Chromosomes

  • Protocol
  • First Online:

  • 1323 Accesses

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1429))

Abstract

Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, Hua A, Giovannoni JJ, Stack SM (2014) Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3 4:1395–1405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Marx V (2013) The genome jigsaw. Nature 501:263–268

    Article  CAS  PubMed  Google Scholar 

  3. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  4. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  5. Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    Article  CAS  PubMed  Google Scholar 

  6. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E et al (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345:1249721

    Article  PubMed  Google Scholar 

  7. Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH (2000) Construction of plant bacterial artificial chromosome (BAC) libraries in plants: an illustrated guide. J Agric Genom 5, http://www.ncgr.org./research/jag

    Google Scholar 

  8. Zhang HB, Woo SS, Wing RA (1996) BAC, YAC and cosmid library construction. In: Foster GD, Twell D (eds) Plant gene isolation: principles and practise. Wiley, New York, pp 75–99

    Google Scholar 

  9. Zhang HB, Zhao XP, Ding XL, Paterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175–184

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  12. Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A (2014) LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Res. doi:10.1093/dnares/dsu042

    PubMed  PubMed Central  Google Scholar 

  13. Allouis S, Moore G, Bellec A, Sharp R, Faivre -Rampant P, Mortimer K, Pateyron S, Foote TN, Griffiths S, Caboche M, Chalhoub B (2003) Construction and characterization of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm ‘Chinese Spring’. Cereal Res Commun 31:331–338

    CAS  Google Scholar 

  14. Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, Doležel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223

    Article  PubMed  Google Scholar 

  15. Doležel J, Šimková H, Šafář J, Kubaláková M, Vrána J, Číhalíková J, Šperková R, Kianian SF, Sourdille P, Lukaszewski AJ, Endo TR, Gill BS (2014) International wheat genome sequencing consortium. A complete set of chromosome BAC libraries for genomics of wheat (Triticum aestivum). In: Abstracts of the International conference “Plant and Animal genome XXII”, Sherago International Inc., San Diego, p. 206

    Google Scholar 

  16. Mago R, Tabe L, Vautrin S, Šimková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Dolezel J, Appels R, Ellis J, Spielmeyer W (2014) Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biol 14:379

    Article  PubMed  PubMed Central  Google Scholar 

  17. Janda J, Šafář J, Kubaláková M, Bartoš J, Kovářová P, Suchánková P, Pateyron S, Číhalíková J, Sourdille P, Šimková H, Fairaivre-Rampant P, Hřibová E, Bernard M, Lukaszewski A, Doležel J, Chalhoub B (2006) Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J 47:977–986

    Article  CAS  PubMed  Google Scholar 

  18. Šimková H, Šafář J, Suchánková P, Kovářová P, Bartoš J, Kubaláková M, Janda J, Číhalíková J, Mago R, Lelley T, Doležel J (2008) A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS). BMC Genomics 9:237

    Article  PubMed  PubMed Central  Google Scholar 

  19. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Habor, NY

    Google Scholar 

Download references

Acknowledgment

This work was supported by grant LO1204 from the National Program of Sustainability I. We also thank Dr. Zbyněk Milec for creating figures and critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic

    Jan Šafář, Hana Šimková & Jaroslav Doležel

Authors
  1. Jan Šafář
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hana Šimková
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jaroslav Doležel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jan Šafář .

Editor information

Editors and Affiliations

  1. University of Minnesota, St. Paul, Minnesota, USA

    Shahryar F. Kianian

  2. University of Minnesota, St. Paul, Minnesota, USA

    Penny M. Avoles Kianian

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Šafář, J., Šimková, H., Doležel, J. (2016). Construction of BAC Libraries from Flow-Sorted Chromosomes. In: Kianian, S., Kianian, P. (eds) Plant Cytogenetics. Methods in Molecular Biology, vol 1429. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3622-9_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-3622-9_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3620-5

  • Online ISBN: 978-1-4939-3622-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation