Skip to main content
SpringerLink
Log in
Book cover

Plant Cytogenetics pp 121–130Cite as

DNA and Chromatin Fiber-Based Plant Cytogenetics

  • Chapter
  • First Online:

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 4))

Abstract

Development of the fluorescence in situ hybridization (FISH) technique revolutionized cytogenetic research. FISH on prepared chromosomes has become the most commonly used technique in plant molecular cytogenetics, especially as a physical mapping tool in plant genome research. Despite its popularity, chromosome-based FISH analysis is limited in its capacity to distinguish DNA probes that separated by less than a few megabases. Development of FISH methods based on extended DNA fibers has dramatically increased the resolving power of this technique to the point where one can identify clones separated by only a few kilobases. In addition to the conventional fiber-FISH analysis, specialized techniques have been developed to prepare DNA or chromatin fibers that are suitable for restriction mapping (optical mapping) or immunofluorescence assays. Fiber-FISH and its derivatives are now used extensively in various mapping and genome research projects.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   249.99
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

Abbreviations

BAC:

Bacterial artificial chromosome

FISH:

Fluorescence in situ hybridization

mtDNA:

Mitochondrial DNA

References

  • Adawy SSM, Stupar RM, Jiang J (2004) Fluorescence in situ hybridization of knob-associated DNA elements analysis reveals multiple loci in one-knob and knobless maize lines. J Histochem Cytochem 52:1113–1116

    Article  CAS  PubMed  Google Scholar 

  • Aston C, Mishra B, Schwartz DC (1999) Optical mapping and its potential for large-scale sequencing projects. Trends Biotech 17:297–302

    Article  CAS  Google Scholar 

  • Backert S, Dorfel P, Borner T (1995) Investigation of plant organellar DNAs by pulsed-field gel electrophoresis. Curr Genet 28:390–399

    Article  CAS  PubMed  Google Scholar 

  • Blower MD, Sullivan BA, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2:319–330

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cheng ZK, Dong F, Langdon T, Ouyang S, Buell CB, Gu MH, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, de Pablo JJ, Graham MD, Coppersmith SN, Goldstein S, Schwartz DC (2004) A microfluidic system for large DNA molecule arrays. Anal Chem 76:5293–5301

    Article  CAS  PubMed  Google Scholar 

  • Feng Q, Zhang YJ, Hao P, Wang SY, Fu G, Huang YC, Li Y, Zhu JJ, Liu YL, Hu X, Jia PX, Zhang Y, Zhao Q, Ying K, Yu SL, Tang YS, Weng QJ, Zhang L, Lu Y, Mu J, Lu YQ, Zhang LS, Yu Z, Fan DL, Liu XH, Lu TT, Li C, Wu YR, Sun TG, Lei HY, Li T, Hu H, Guan JP, Wu M, Zhang RQ, Zhou B, Chen ZH, Chen L, Jin ZQ, Wang R, Yin HF, Cai Z, Ren SX, Lv G, Gu WY, Zhu GF, Tu YF, Jia J, Zhang Y, Chen J, Kang H, Cen XY, Shao CY, Sun Y, Hu QP, Zhang XL, Zhang W, Wang LJ, Ding CW, Sheng HH, Gu JL, Chen ST, Ni L, Zhu FH, Chen W, Lan LF, Lai Y, Cheng ZK, Gu MH, Jiang, JM, Li, JY, Hong GF, Xue YB, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320

    Article  CAS  PubMed  Google Scholar 

  • Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJM, Zabel P, de Jong JH (1996) High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9:421–430

    Article  CAS  PubMed  Google Scholar 

  • Haaf T, Ward DC (1994) Structural analysis of alpha satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Mol Genet 3:697–709

    Article  CAS  PubMed  Google Scholar 

  • Houben A, Schroeder-Reiter E, Nagaki K, Nasuda S, Wanner G, Murata M, and Endo TR (2007) CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116:275–283

    Article  CAS  PubMed  Google Scholar 

  • Jackson SA, Wang ML, Goodman HM, Jiang J (1998) Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41:566–572

    CAS  PubMed  Google Scholar 

  • Jackson SA, Dong FG, Jiang JM (1999) Digital mapping of bacterial artificial chromosomes by fluorescence in situ hybridization. Plant J 17:581–587

    Article  CAS  PubMed  Google Scholar 

  • Jackson SA, Zhang P, Chen WP, Phillips RL, Friebe B, Muthukrishnan S, Gill BS (2001) High-resolution structural analysis of biolistic transgene integration into the genome of wheat. Theor Appl Genet 103:56–62

    Article  CAS  Google Scholar 

  • Jiang JM, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068

    Article  CAS  PubMed  Google Scholar 

  • Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570–575

    Article  CAS  PubMed  Google Scholar 

  • Jin WW, Melo JR, Nagaki K, Talbert PB, Henikoff S, Dawe RK, Jiang J (2004) Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell 16:571–581

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jin WW, Lamb JC, Vega JM, Dawe RK, Birchler JA, Jiang J (2005) Molecular and functional dissection of the maize B centromere. Plant Cell 17:1412–1423

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE (2008) Fine-scale mapping and sequencing of structural variation from eight human genomes. Nature 453:56–64

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li HF, Valouev A, Schwartz DC, Waterman MS, Li LM (2007) A quantile method for sizing optical maps. J Comput Biol 14:255–266

    Article  PubMed  Google Scholar 

  • Lilly JW, Havey MJ, Jackson SA, Jiang J (2001) Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell 13:245–254

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lin JY, Jacobus BH, SanMiguel P, Walling JG, Yuan Y, Shoemaker RC, Young ND, Jackson SA (2005) Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170:1221–1230

    Article  CAS  PubMed  Google Scholar 

  • Lin XY, Kaul SS, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402:761–768

    Article  CAS  PubMed  Google Scholar 

  • Nagaki K, Song J, Stupar SM, Parokonny AS, Yuan Q, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang J (2003) Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163:759–770

    CAS  PubMed  Google Scholar 

  • Nakano A, Suzuki G, Yamamoto M, Turnbull K, Rahman S, Mukai Y (2005) Rearrangements of large-insert T-DNAs in transgenic rice. Mol Genet Genomics 273:123–129

    Article  CAS  PubMed  Google Scholar 

  • Ohmido N, Kijima K, Akiyama Y, de Jong JH, Fukui K (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet 263:388–394

    Article  CAS  PubMed  Google Scholar 

  • Phan BH, Jin WW, Topp CN, Zhong CX, Jiang JM, Dawe RK, Parrott WA (2007) Transformation of rice with long DNA-segments consisting of random genomic DNA or centromere-specific DNA. Transgenic Res 16:341–351

    Article  CAS  PubMed  Google Scholar 

  • Pich U, Schubert I (1998) Terminal heterochromatin and alternative telomeric sequences in Allium cepa. Chromosome Res 6:315–321

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu JZ, Niimura Y, Cheng ZK, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Msukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukae Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song JY, Takazaki Y, Terasawa K, Tsuji, K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong HS, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang JM, Gojohori T (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316

    Article  CAS  PubMed  Google Scholar 

  • Schwartz DC, Li XJ, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114

    Article  CAS  PubMed  Google Scholar 

  • Shibata F, Murata M (2004) Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci 117:2963–2970

    Article  CAS  PubMed  Google Scholar 

  • Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci USA 98:5099–5103

    Article  CAS  PubMed  Google Scholar 

  • Sullivan BA, Karpen GH (2004) Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struct Mol Biol 11:1076–1083

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Svitashev SK, Somers DA (2001) Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment. Genome 44:691–697

    Article  CAS  PubMed  Google Scholar 

  • Tek AL, Jiang J (2004) The centromeric regions of potato chromosomes contain megabase-sized tandem arrays of telomere-similiar sequence. Chromosoma 113:77–83

    Article  CAS  PubMed  Google Scholar 

  • Wolters A-MA, Trindade LM, Jacobsen E, Visser RGF (1998) Fluorescence in situ hybridization on extended DNA fibers as a tool to analyze complex T-DNA loci in potato. Plant J 13:837–847

    Article  CAS  Google Scholar 

  • Yan HH, Ito H, Nobuta K, Ouyang S, Jin WW, Tian SL, Lu C, Venu RC, Wang G-L, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang J (2006) Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123–2133

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yu WC, Han FP, Gao Z, Vega JM, Birchler JA (2007) Construction and behavior of engineered minichromosomes in maize. Proc Natl Acad Sci USA 104:8924–8929

    Article  CAS  PubMed  Google Scholar 

  • Yu YS, Rambo T, Currie J, Saski C, Kim HR, Collura K, Thompson S, Simmons J, Yang TJ, Nah G, Patel AJ, Thurmond S, Henry D, Oates R, Palmer M, Pries G, Gibson J, Anderson H, Paradkar M, Crane L, Dale J, Carver MB, Wood T, Frisch D, Engler F, Soderlund C, Palmer LE, Tetylman L, Nascimento L, de la Bastide M, Spiegel L, Ware D, O’Shaughnessy A, Dike S, Dedhia N, Preston R, Huang E, Ferraro K, Kuit K, Miller B, Zutavern T, Katzenberger F, Muller S, Balija V, Martienssen RA, Stein L, Minx P, Johnson D, Cordum H, Mardis E, Cheng ZK, Jiang JM, Wilson R, McCombie Wr, Wing RA, Yuan QP, Su OY, Liu J, Jones KM, Gansberger K, Moffat K, Hill J, Tsitrin T, Overton L, Bera J, Kim M, Jin SH, Tallon L, Ciecko A, Pai G, Van Aken S, Utterback T, Reidmuller S, Bormann J, Feldblyum T, Hsiao J, Zismann V, Blunt S, de Vazeilles A, Shaffer T, Koo H, Suh B, YangQ, Haas B, Peterson J, Pertea M, Volfovsky N, Wortman J, White O, Salzberg SL, Fraser CM, Buell CR, Messing J, Song RT, Fuks G, Llaca V, Kovchak S, Young S, Bowers JE, Paterson AH, Johns MA, Mao L, Pan HW, Dean RA (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569

    Article  CAS  Google Scholar 

  • Yuan Q, Hill J, Hsiao J, Moffat K, Ouyang S, Cheng Z, Jiang J, Buell CR (2002) Genome sequencing of a 239-kb region of rice chromosome 10 L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics 267:713–720

    Article  CAS  PubMed  Google Scholar 

  • Zhang WL, Lee H-R, Koo D-H, Jiang JM (2008) Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 20:25–34

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhong XB, Fransz PF, Wennekes-van Eden J, Ramanna MS, van Kammen A, Zabel P, de Jong JH (1998) FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J 13:507–517

    Article  CAS  PubMed  Google Scholar 

  • Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest DK, Goldstein S, Livny M, Schwartz DC (2007) Validation of rice genome sequence by optical mapping. BMC Genomics 8: Art. No. 278

    Google Scholar 

Download references

Acknowledgments

We are grateful to Drs. David C. Schwartz and Shiguo Zhou for their input on our summary of optical mapping and for providing the image in Fig. 5.2. The most recent cytogenetic mapping research in the authors’ laboratory has been supported by grants DBI-0421671 and DBI-0603927 from the National Science Foundation.

Author information

Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Jason G. Walling & Jiming Jiang

Authors
  1. Jason G. Walling
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiming Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jason G. Walling .

Editor information

Editors and Affiliations

  1. Department of Biological Science, Florida State University, Tallahassee, Florida, USA

    Hank W. Bass

  2. Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA

    James A. Birchler

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Walling, J.G., Jiang, J. (2012). DNA and Chromatin Fiber-Based Plant Cytogenetics. In: Bass, H., Birchler, J. (eds) Plant Cytogenetics. Plant Genetics and Genomics: Crops and Models, vol 4. Springer, New York, NY. https://doi.org/10.1007/978-0-387-70869-0_5

Download citation

Publish with us

Policies and ethics

Search

Navigation