Applied Cytogenetics

  • R. Kelly DaweEmail author
Part of the Biotechnology in Agriculture and Forestry book series (AGRICULTURE, volume 63)

Historically, most cytogenetics was carried out on (meiotic) pachytene cells where individual chromosomes can be readily identified (e.g. Anderson et al. 2004). A weakness of pachytene analysis is that whole plants must be grown to near maturity to collect samples. Root tip chromosomes offer a simpler way to collect chromosome information, but they have been viewed as too small to accurately identify chromosome variants and cytological features.

The power of mitotic chromosome analysis changed dramatically with the discovery of new FISH methods to label and identify root tip chromosomes. Birchler and colleagues showed that by mixing a collection of repetitive probes labeled with differently colored tags (fluorophores) it was possible to rapidly identify all ten maize chromosomes (Kato et al. 2004). They also introduced an important nitrous oxide method for increasing the number of condensed chromosomes from a single root tip. Subsequently, the same group went on to show that the sensitivity of FISH could be increased dramatically by increasing the amount of a key enzyme (DNA polymerase) in the labeling protocol (Kato et al. 2006).


Maize Chromosome Pachytene Chromosome Pachytene Cell Pachytene Analysis Engineer Chromosome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Alvarez-Venegas R, Avramova Z (2005) Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants. Nucleic Acids Res 33:5199–5207PubMedCrossRefGoogle Scholar
  2. Amarillo FI, Bass HW (2007) A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion. Genetics 177:1509–1526PubMedCrossRefGoogle Scholar
  3. Anderson LK, Salameh N, Bass HW, Harper LC, Cande WZ, Weber G, Stack SM (2004) Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics 166:1923–1933PubMedCrossRefGoogle Scholar
  4. Basu J, Willard HF (2005) Artificial and engineered chromosomes: non-integrating vectors for gene therapy. Trends Mol Med 11:251–258PubMedCrossRefGoogle Scholar
  5. Carlson SR, Rudgers GW, Zieler H, Mach JM, Luo S, Grunden E, Krol C, Copenhaver GP, Preuss D (2007) Meiotic transmission of an in vitro-assembled autonomous maize minichromosome. PLOS Genet 3:1965–1974PubMedCrossRefGoogle Scholar
  6. Carlson WR (1986) The B-chromosome of maize. Crit Rev Plant Sci 3:201–226CrossRefGoogle Scholar
  7. Choo KH (2001) Domain organization at the centromere and neocentromere. Dev Cell 1: 165–177PubMedCrossRefGoogle Scholar
  8. Danker T, Dreesen B, Offermann S, Horst I, Peterhansel C (2008) Developmental information but not promoter activity controls the methylation state of histone H3 lysine 4 on two photosynthetic genes in maize. Plant J 53(3):456–474CrossRefGoogle Scholar
  9. Dawe RK (1998) Meiotic chromosome organization and segregation in plants. Ann Rev Plant Phys Plant Mol Biol 49:371–395CrossRefGoogle Scholar
  10. Dawe RK (2005) Centromere renewal and replacement in the plant kingdom. Proc Natl Acad Sci USA 102:11573–11574PubMedCrossRefGoogle Scholar
  11. Earley KW, Shook MS, Brower-Toland B, Hicks L, Pikaard CS (2007) In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J 52:615–626PubMedCrossRefGoogle Scholar
  12. Ebert A, Lein S, Schotta G, Reuter G (2006) Histone modification and the control of heterochro-matic gene silencing in Drosophila. Chromosome Res 14:377–392PubMedCrossRefGoogle Scholar
  13. Farr C, Fantes J, Goodfellow P, Cooke H (1991) Functional reintroduction of human telomeres into mammalian cells. Proc Natl Acad Sci USA 88:7006–7010PubMedCrossRefGoogle Scholar
  14. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets ge-nomics. Nat Rev Genet 3:329–341PubMedCrossRefGoogle Scholar
  15. Han F, Gao Z, Yu W, Birchler JA (2007) Minichromosome analysis of chromosome pairing, disjunction, and sister chromatid cohesion in maize. Plant Cell 19:3853–3863PubMedCrossRefGoogle Scholar
  16. Haring M, Offermann S, Danker T, Horst I, Peterhansel C, Stam M (2007) Chromatin im-munoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:11PubMedCrossRefGoogle Scholar
  17. Harrington JJ, Bokkelen GV, Mays RW, Gustashaw K, Willard HF (1997) Formation of de novo centromeres and construction of first-generation human artificial chromosomes. Nature Genetics 15:345–355PubMedCrossRefGoogle Scholar
  18. Hernandez JM, Feller A, Morohashi K, Frame K, Grotewold E (2007) The basic helix-loop-helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor. Proc Natl Acad Sci USA 104:17222–17227PubMedCrossRefGoogle Scholar
  19. Houben A, Schubert I (2007) Engineered plant minichromosomes: a resurrection of B chromosomes? Plant Cell 19:2323–2327PubMedCrossRefGoogle Scholar
  20. Houben A, Demidov D, Gernand D, Meister A, Leach CR, Schubert I (2003) Methylation of his-tone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J 33:967–973PubMedCrossRefGoogle Scholar
  21. Houben A, Dawe R, Jiang J, Schubert I (2008) Engineered plant minichromosomes — a bottom-up success? Plant Cell 20:8–10PubMedCrossRefGoogle Scholar
  22. Irvine DV, Shaw ML, Choo KH, Saffery R (2005) Engineering chromosomes for delivery of therapeutic genes. Trends Biotechnol 23:575–583PubMedCrossRefGoogle Scholar
  23. Jin W, 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 16:571–581PubMedCrossRefGoogle Scholar
  24. Karpen GH, Allshire RC (1997) The case of epigenetic effects on centromere identity and function. Trends Genet 13:489–496PubMedCrossRefGoogle Scholar
  25. Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177:1975–1985PubMedCrossRefGoogle Scholar
  26. Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101:13554–13559PubMedCrossRefGoogle Scholar
  27. Kato A, Albert PS, Vega JM, Birchler JA (2006) Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81:71–78PubMedCrossRefGoogle Scholar
  28. Lamb JC, Birchler JA (2006) Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 173:1007–1021PubMedCrossRefGoogle Scholar
  29. Lamb JC, Meyer JM, Birchler JA (2007a) A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region. Chromosoma 116:237–247CrossRefGoogle Scholar
  30. Lamb JC, Danilova T, Bauer MJ, Meyer JM, Holland JJ, Jensen MD, Birchler JA (2007b) Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175:1047–1058CrossRefGoogle Scholar
  31. Lim HN, Farr CJ (2004) Chromosome-based vectors for Mammalian cells: an overview. Methods Mol Biol 240:167–186PubMedGoogle Scholar
  32. Loidl P (2004) A plant dialect of the histone language. Trends Plant Sci 9:84–90PubMedCrossRefGoogle Scholar
  33. Luce AC, Sharma A, Mollere OS, Wolfgruber TK, Nagaki K, Jiang J, Presting GG, Dawe RK (2006) Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction. Genetics 174:1057–1061PubMedCrossRefGoogle Scholar
  34. Malik HS, Henikoff S (2001) Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics 157:1293–1298PubMedGoogle Scholar
  35. Matzke MA, Matzke AJM (2004) Planting the seeds of a new paradigm. PLOS Biol 2:582–586CrossRefGoogle Scholar
  36. Mito Y, Henikoff JG, Henikoff S (2005) Genome-scale profiling of histone H3.3 replacement patterns. Nat Genetics 37:1090–1097CrossRefGoogle Scholar
  37. Mito Y, Henikoff JG, Henikoff S (2007) Histone replacement marks the boundaries of cis-regulatory domains. Science 315:1408–1411PubMedCrossRefGoogle Scholar
  38. Nasuda S, Hudakova S, Schubert I, Houben A, Endo TR (2005) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102:9842–9847PubMedCrossRefGoogle Scholar
  39. Shi J, Dawe K (2006) Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173:1571–1583PubMedCrossRefGoogle Scholar
  40. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45PubMedCrossRefGoogle Scholar
  41. Suzuki N, Nishii K, Okazaki T, Ikeno M (2006) Human artificial chromosomes constructed using the bottom-up strategy are stably maintained in mitosis and efficiently transmissible to progeny mice. J Biol Chem 281:26615–26623PubMedCrossRefGoogle Scholar
  42. Wang CJ, Harper L, Cande WZ (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18:529–544PubMedCrossRefGoogle Scholar
  43. Wieland G, Orthaus S, Ohndorf S, Diekmann S, Hemmerich P (2004) Functional complementation of human centromere protein A (CENP-A) by Cse4p from Saccharomyces cerevisiae. Mol Cell Biol 24:6620–6630PubMedCrossRefGoogle Scholar
  44. Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17:3227–3238PubMedCrossRefGoogle Scholar
  45. Yan HH, Ito H, Nobuta K, Ouyang S, Jin WW, Tian SL, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang JM (2006) Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123–2133PubMedCrossRefGoogle Scholar
  46. Yu W, Lamb JC, Han F, Birchler JA (2006) Telomere-mediated chromosomal truncation in maize. Proc Natl Acad Sci USA 103:17331–17336PubMedCrossRefGoogle Scholar
  47. Yu W, Lamb JC, Han F, Birchler JA (2007a) Cytological visualization of DNA transposons and their transposition pattern in somatic cells of maize. Genetics 175:31–39CrossRefGoogle Scholar
  48. Yu W, Han F, Gao Z, Vega JM, Birchler JA (2007b) Construction and behavior of engineered minichromosomes in maize. Proc Natl Acad Sci USA 104:8924–8929CrossRefGoogle Scholar
  49. Zhang XY, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLOS Biol 5:1026–1035Google Scholar
  50. Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825–2836PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, B.V 2009

Authors and Affiliations

  1. 1.Department of Plant Biology, Miller Plant Sciences BldgUniversity of GeorgiaAthensUSA

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