Skip to main content

Molecular Cytogenetics (FISH and Fluorochrome Banding): Resolving Species Relationships and Genome Organization

  • Protocol
  • First Online:
Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

Fluorochrome banding (chromomycin, Hoechst, and DAPI) and fluorescence in situ hybridization (FISH) are excellent molecular cytogenetic tools providing various possibilities in the study of chromosomal evolution and genome organization. The constitutive heterochromatin and rRNA genes are the most widely used FISH markers. The rDNA is organized into two distinct gene families (18S-5.8S-26S and 5S) whose number and location vary within the complex of closely related species. Therefore, they are widely used as chromosomal landmarks to provide valuable evidence concerning genome evolution at chromosomal levels.

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

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

Institutional subscriptions

Similar content being viewed by others

References

  1. Murata M, Heslop-Harrison JS, Motoyoushi F (1997) Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones. Plant J 12(1):31–37

    Article  CAS  PubMed  Google Scholar 

  2. Cerbah M, Kevei Z, Siljak-Yakovlev S et al (1998) rDNA organization and heterochromatin pattern in Medicago truncatula. Cytogenet Cell Genet 81:141

    Google Scholar 

  3. Siljak-Yakovlev S, Cerbah M, Couland J et al (2002) Nuclear DNA content, base composition, heterochromatin and rDNA in Picea omorika and Picea abies. Theor Appl Genet 104:505–512

    Article  CAS  PubMed  Google Scholar 

  4. Cerbah M, Coulaud J, Siljak-Yakovlev S (1998) rDNA organization and evolutionary relationships in the genus Hypochaeris (Asteraceae). J Hered 89:312–318

    Article  CAS  Google Scholar 

  5. Weiss-Schneeweiss H, Tremetsberger K, Schneeweiss GM, Parker JS, Stuessy TF (2008) Karyotype diversification and evolution in diploid and polyploid South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data. Ann Bot 101: 909–918

    Article  CAS  PubMed  Google Scholar 

  6. Zoldos V, Papes D, Cerbah M et al (1999) Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among eleven Quercus species. Theor Appl Genet 99:969–977

    Article  CAS  Google Scholar 

  7. Siljak-Yakovlev S, Peccenini S, Muratovic E et al (2003) Chromosomal differentiation and genome size in three European mountain Lilium species. Plant Syst Evol 236:165–173

    Article  CAS  Google Scholar 

  8. Lim KY, Matyásek R, Lichtenstein CP et al (2000) Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109:245–258

    Article  CAS  PubMed  Google Scholar 

  9. Bogunic F, Siljak-Yakovlev S, Muratovic E et al (2011) Different karyotype patterns among allopatric Pinus nigra (Pinaceae) populations revealed by molecular cytogenetics. Plant Biol 13:194–200

    Article  CAS  PubMed  Google Scholar 

  10. Bogunic F, Siljak-Yakovlev S, Muratovic E et al (2011) Molecular cytogenetics and flow cytometry reveal conserved genome organization in Pinus mugo and P. uncinata. Ann For Sci 68(1):179–187

    Article  Google Scholar 

  11. Hizume M, Aria M, Tanaka A (1990) Chromosome banding in the genus Pinus. III. Fluorescent banding pattern of P. luchuensis and its relationships among the Japanese diploxylon pines. Bot Mag Tokyo 103:103–111

    Article  Google Scholar 

  12. Bogunic F, Muratovic E, Siljak-Yakovlev S (2006) Chromosomal differentiation of Pinus heldreichii and Pinus nigra. Ann For Sci 63:267–274

    Article  Google Scholar 

  13. Muratovic E, Robin O, Bogunic F et al (2010) Speciation of European lilies from Liriotypus section based on karyotype evolution. Taxon 59:165–175

    Google Scholar 

  14. Godelle B, Cartier D, Marie D et al (1993) Heterochromatin study demonstrating the non-linearity of fluorometry useful for calculating genomic base composition. Cytometry 14:618–626

    Article  CAS  PubMed  Google Scholar 

  15. Sell PD (1976) Crepis. In: Tutin TG et al (eds) Flora Europaea 4. Cambridge University Press, Cambridge, pp 344–357

    Google Scholar 

  16. Siljak-Yakovlev S, Cartier D (1986) Heterochromatin patterns in some taxa of Crepis praemorsa complex. Caryologia 39:27–32

    Article  Google Scholar 

  17. Cartier D, Siljak-Yakovlev S (1992) Cytogenetics study of the F1 hybrids between Crepis dinarica and Crepis froelichiana. Plant Syst Evol 182:29–34

    Article  Google Scholar 

  18. Schwarzacher T, Heslop-Harrison P (2000) Practical in situ hybridization, 2nd edn. BIOS, Oxford, UK

    Google Scholar 

  19. Schubert I, Wobus U (1985) In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma 92: 143–148

    Article  Google Scholar 

  20. Raina SN, Mukai Y (1999) Detection of a variable number of 18S-5.8S-26S and 5S ribosomal DNA loci by fluorescent in situ hybridization in diploid and tetraploid Arachis species. Genome 42:52–59

    Article  CAS  Google Scholar 

  21. Raskina O, Belyayev A, Nevo E (2004) Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc Natl Acad Sci USA 101:14818–14823

    Article  CAS  PubMed  Google Scholar 

  22. Datson PM, Murray BG (2006) Ribosomal DNA locus evolution in Nemesia: transposition rather than structural rearrangement as the key mechanism? Chromosome Res 14: 845–857

    Article  CAS  PubMed  Google Scholar 

  23. Geber G, Schweizer D (1988) Cytochemical heterochromatin differentiation in Sinapis alba (Cruciferae) using a simple air-drying technique for producing chromosome spreads. Plant Syst Evol 158:97–106

    Article  CAS  Google Scholar 

  24. Conger AD, Fairchild LM (1953) A quick freeze method for making smear slides. Stain Technol 28:281–283

    CAS  PubMed  Google Scholar 

  25. Schweiser D (1976) Reverse fluorescent chromosome banding with chromomycin and DAPI. Chromosoma 58:307–324

    Article  Google Scholar 

  26. Kondo T, Hizume M (1982) Banding for the chromosomes of Cryptomeria japonica D. Don. J Jpn For Soc 64:356–358

    Google Scholar 

  27. Martin J, Hesemann CU (1988) Evaluation of improved Giemsa C- and fluorochrome banding techniques in rye chromosome. Heredity 6:459–467

    Article  Google Scholar 

  28. Heslop-Harrison LS, Schwarzacher T, Anamthawat-Jonsson K et al (1991) In situ hybridization with automated chromosome denaturation. Techniques 3:109–116

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer New York

About this protocol

Cite this protocol

Siljak-Yakovlev, S., Pustahija, F., Vicic, V., Robin, O. (2014). Molecular Cytogenetics (FISH and Fluorochrome Banding): Resolving Species Relationships and Genome Organization. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-767-9_15

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-766-2

  • Online ISBN: 978-1-62703-767-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics