Skip to main content
SpringerLink
Log in

Organelle DNA isolation and RFLP analysis

  • Chapter
Plant Genomes: Methods for Genetic and Physical Mapping

Abstract

The analysis of restriction fragment length polymorphisms (RFLPs) in organelle DNA is radically different from that in nuclear DNA in both purpose and execution. The fundamental reason for these differences is genome size: in land plants, chloroplast DNA (cpDNA) is 1-2 x 102 kb in size [38, 39] and mitochondrial DNA (mtDNA) 2-20 x 102 kb [14, 26, 37, 39], whereas most nuclear genomes are 1-10 x 106 kb [2]. The larger size of nuclear genomes is reflected in our relatively poor understanding of their structure and the fact that only a small fraction of nuclear genes have been isolated and analyzed. Physical mapping of RFLPs for an entire, average-sized nuclear genome is a forbidding task whose completion is at least several years away, and the physical mapping of even a 1 % region of the genome presents a significant challenge. As a consequence, nuclear RFLPs are presently used primarily as genetic markers in linkage studies aimed at identifying and selecting traits of agronomic importance [27, 44] and at examining modes of chromosomal evolution [15, 54]. Nuclear RFLPs are just beginning to be used as physical markers in chromosome walking efforts to clone mapped genes of interest [58].

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

Access this chapter

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 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bendich AI (1987) Why do chloroplasts and mitochondria contain so many copies of their genome? Bioessays 6: 279–282.

    Article  PubMed  CAS  Google Scholar 

  2. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Trans Roy Soc Ser B 274: 227–274.

    Article  CAS  Google Scholar 

  3. Bookjans G, Stummann BM, Henningsen KW (1984) Preparation of chloroplast DNA from pea plastids isolated in a medium of high ionic strength. Anal Biochem 141: 244–247.

    Article  PubMed  CAS  Google Scholar 

  4. Bowman DM, Dyer TA (1982) Purification and analysis of DNA from wheat chloroplasts isolated in nonaqueous media. Anal Biochem 122: 108–118.

    Article  PubMed  CAS  Google Scholar 

  5. Calie PJ, Hughes KW (1987) An efficient protocol for the isolation and purification of chloroplast DNA from moss gametophyte tissues. Plant Mol Biol Rep 4: 206–212.

    Article  CAS  Google Scholar 

  6. Crawford DJ (1990) Plant Molecular Systematics: Macromolecular Approaches. New York: Wiley.

    Google Scholar 

  7. Dally AM, Second G (1989) Chloroplast DNA isolation from higher plants: An improved non-aqueous method. Plant Mol Biol Rep 7: 135–143.

    Article  CAS  Google Scholar 

  8. Delaney TP, Cattolico RA (1989) Chloroplast ribosomal DNA organization in the chromophytic alga Olisthodiscus luteus. Curr Genet 15: 221–229.

    Article  PubMed  CAS  Google Scholar 

  9. Douglas SE (1988) Physical mapping of the plastid genome from the chlorophyll c-containing alga, Cryptomonas sp. Curr Genet 14: 591–598.

    Article  CAS  Google Scholar 

  10. Dowling TE, Moritz C, Palmer JD (1990) Nucleic acids 11: restriction site analysis. In: Hillis D, Moritz C (eds) Molecular Systematics, pp. 250–317. Sunderland: Sinauer.

    Google Scholar 

  11. Downie SR, Palmer JD (1992) Use of chloroplast DNA re arrangements in reconstructing plant phylogeny. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular Systematics of Plants, pp. 14–35. New York: Chapman and Hall.

    Chapter  Google Scholar 

  12. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11–15.

    Google Scholar 

  13. Gillham NW, Boynton JE, Harris EH (1991) Transmission of plastid genes. In: Bogorad L, Vasil IK (eds.) Cell Culture and Somatic Cell Genetics of Plants, Vol. 7A, The Molecular Biology of Plastids, pp. 55–92. New York: Academic Press.

    Google Scholar 

  14. Gray MW (1989) Origin and evolution of mitochondrial DNA. Annu Rev Cell Biol 5: 25–50.

    Article  PubMed  CAS  Google Scholar 

  15. Helentjaris T, Weber D, Wright S (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353–363.

    PubMed  CAS  Google Scholar 

  16. Herrmann RG (1982) The preparation of circular DNA from plastids. In: Edelman M, Hallick R, Chua NH (eds) Methods in Chloroplast Molecular Biology, pp. 259–280. Amsterdam: Elsevier.

    Google Scholar 

  17. Hiratsu J, Shimada H, Whittier RF, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217: 185–194

    Article  Google Scholar 

  18. Hsu CL, Mullin BC (1988) A new protocol for isolation of mitochondrial DNA from cotton seedlings. Plant Cell Rep 7: 356–360.

    Article  CAS  Google Scholar 

  19. Jansen RK, Palmer JD (1987) A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc Natl Acad Sci USA 84: 5818–5822.

    Article  PubMed  CAS  Google Scholar 

  20. Kemble RJ (1987) A rapid, single leaf, nucleic acid assay for determining the cytoplasmic organelle complement of rapeseed and related Brassica species. Theor Appl Genet 73: 364–370.

    Article  CAS  Google Scholar 

  21. Kolodner R, Tewari KK (1972) Physicochemical characterization of mitochondrial DNA from pea leaves. Proc Natl Acad Sci USA 69: 1830–1834.

    Article  PubMed  CAS  Google Scholar 

  22. Kolodner R, Tewari KK (1975) The molecular size and conformation of the chloroplast DNA from higher plants. Biochim Biophys Acta 402: 372–390.

    Article  PubMed  CAS  Google Scholar 

  23. Kolodner R, Tewari KK, Warner RC (1976) Physical studies on the size and structure of the covalently closed circular chloroplast DNA from higher plants. Biochim Biophys Acta 447: 144–155.

    Article  PubMed  CAS  Google Scholar 

  24. Lavin M, Doyle JJ, Palmer JD (1990) Evolutionary significance of the loss of the chloroplast DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 44: 390–402.

    Article  CAS  Google Scholar 

  25. Lemieux C, Turmel M, Seligy VL, Lee RW (1984) Chloroplast DNA recombination in interspecific hybrids of Chlamydomonas: Linkage between a non-Mendelian locus for streptomycin resistance and restriction fragments coding for 16S rRNA. Proc Natl Acad Sci USA 81: 1164–1168.

    Article  PubMed  CAS  Google Scholar 

  26. Lonsdale DM (1989) The plant mitochondrial genome. In: Marcus A (ed), Biochemistry of Plants, Vol. 15, Molecular Biology, pp. 229–295. New York: Academic Press.

    Google Scholar 

  27. Martin B, Nienhuis J, King G, Schaefer A (1989) Restriction fragment length polymorphisms associated with water use efficiency in tomato. Science 243: 1725–1728.

    Article  PubMed  CAS  Google Scholar 

  28. Milligan BG (1989) Purification of chloroplast DNA using hexadecyltrimethylammonium bromide. Plant Mol Biol Rep 7: 144–149.

    Article  CAS  Google Scholar 

  29. Mourad G, Polacco ML (1989) Mini-preparation of highly purified chloroplast DNA from maize. Plant Mol Biol Rep 7: 78–84.

    Article  CAS  Google Scholar 

  30. Neale DB, Sederoff RR (1988) Inheritance and evolution of conifer organelle genomes. In: Hanover JW, Keathley DE (eds) Genetic Manipulation of Woody Plants, pp. 251–264. New York: Plenum.

    Chapter  Google Scholar 

  31. Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano H, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572–574.

    Article  CAS  Google Scholar 

  32. Palmer JD (1982) Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativa. Nucleic Acids Res 10: 1593–1605.

    Article  PubMed  CAS  Google Scholar 

  33. Palmer JD (1985) Evolution of chloroplast and mitochondrial DNA in plants and algae. In: Maclntyre RJ (ed) Monographs in Evolutionary Biology: Molecular Evolutionary Genetics, pp. 131–240. New York: Plenum.

    Google Scholar 

  34. Palmer JD (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19: 325–354.

    Article  PubMed  CAS  Google Scholar 

  35. Palmer JD (1986) Isolation and structural analysis of chloroplast DNA. Meth Enzymol 118: 167–186.

    Article  CAS  Google Scholar 

  36. Palmer JD (1987) Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. Am Natur 130: S6–S29.

    Article  CAS  Google Scholar 

  37. Palmer JD (1990) Contrasting modes and tempos of genome evolution in plant organelles. Trends Genet 6: 115–120.

    Article  PubMed  CAS  Google Scholar 

  38. Palmer JD (1992) Plastid chromosomes: structure and evolution. In: Bogorad L, Vasil IK (eds) Cell Culture and Somatic Cell Genetics of Plants, Vol. 7 A, The Molecular Biology of Plastids, pp. 5–53. New York: Academic Press.

    Google Scholar 

  39. Palmer JD (1992) Chloroplast and mitochondrial genome evolution in land olants. In: Herrmann RG (ed) Plant Gene Research, Vol. 6, Organelles, in press. New York: Springer-Verlag.

    Google Scholar 

  40. Palmer JD (1992) Mitochondrial DNA in plant systematics: applications and limitations. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular Systematics of Plants, pp. 36–49. New York: Chapman and Hall.

    Chapter  Google Scholar 

  41. Palmer JD, Herbon LA (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 28: 87–97.

    Article  PubMed  CAS  Google Scholar 

  42. Palmer JD, Jorgensen RA, Thompson WF (1985) Chloroplast DNA variation and evolution in Pisum: Patterns of change and phylogenetic analysis. Genetics 109: 195–213.

    PubMed  CAS  Google Scholar 

  43. Palmer JD, Jansen RK, Michaels HJ, Chase MW, Manhart JR (1988) Chloroplast DNA variation and plant phylogeny. Ann Missouri Bot Gard 75: 1180–1206.

    Article  Google Scholar 

  44. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726.

    Article  PubMed  CAS  Google Scholar 

  45. Price CA, Cushman JC, Mendiola-Morgenthaler LR, Reardon EM (1987) Isolation of plastids in density gradients of percoll and other silica sols. Meth Enzymol 148: 157–179.

    Article  CAS  Google Scholar 

  46. Robertson D, Palmer JD, Earle ED, Mutschier MA (1987) Analysis of organelle genomes in a somatic hybrid derived from cytoplasmic male-sterile Brassica oleracea and atrazine-resistant B. campestris. Theor Appl Genet 74: 303–309.

    Article  Google Scholar 

  47. Rothenberg M, Hanson MR (1987) Recombination between parental mitochondrial DNA following protoplast fusion can occur in a region which normally does not undergo intragenomic recombination in parental plants. Curr Genet 12: 235–240.

    Article  CAS  Google Scholar 

  48. Sandbrink JM, Vellekoop P, Van Harn R, Van Brederode J (1989) A method for evolutionary studies on RFLP of chloroplast DNA, applicable to a range of plant species. Biochem Syst Ecol 17: 45–49.

    Article  CAS  Google Scholar 

  49. Sears BB (1980) The elimination of plastids during spermatogenesis and fertilization in the plant kingdom. Plasmid 4: 233–255.

    Article  PubMed  CAS  Google Scholar 

  50. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of tobacco chloroplast genome: Hs gene organization and expression. EMBO J 5: 2043–2049.

    PubMed  CAS  Google Scholar 

  51. Smith GE, Summers MD (1980) The bidirectional transfer of DNA and RNA to nitrocellulose or diazobenzyloxymethyl paper. Anal Biochem 109: 123–129.

    Article  PubMed  CAS  Google Scholar 

  52. Soltis PS, Soltis DE, Doyle JJ (1992) Molecular Systematics of Plants. New York: Chapman and Hall.

    Book  Google Scholar 

  53. Stern DB, Palmer JD (1984) Extensive and widespread homologies between mitochondrial and chloroplast DNA in plants. Proc Natl Acad Sci USA 81: 1946–1950.

    Article  PubMed  CAS  Google Scholar 

  54. Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85: 6419–6423.

    Article  PubMed  CAS  Google Scholar 

  55. Tewari KK, Wildman SG (1966) Chloroplast DNA from tobacco leaves. Science 153: 1269–1271.

    Article  PubMed  CAS  Google Scholar 

  56. White EE (1986) A method for extraction of chloroplast DNA from conifers. Plant Mol Biol Rep 4: 98–101.

    Article  CAS  Google Scholar 

  57. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitutions vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84: 9054–9058.

    Article  PubMed  CAS  Google Scholar 

  58. Young ND, Zamir D, Ganal MW, Tanksley SD (1988) Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the Tm-2a gene in tomato. Genetics 120: 579–585.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, 47405, USA

    Jeffrey D. Palmer

Authors
  1. Jeffrey D. Palmer
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Plant Genetics and Breeding, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel

    J. S. Beckmann

  2. Department of Agronomy, University of Wisconsin, Madison, WI, USA

    T. C. Osborn

Rights and permissions

Reprints and permissions

Copyright information

© 1992 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Palmer, J.D. (1992). Organelle DNA isolation and RFLP analysis. In: Beckmann, J.S., Osborn, T.C. (eds) Plant Genomes: Methods for Genetic and Physical Mapping. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-2442-3_3

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-2442-3_3

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5077-7

  • Online ISBN: 978-94-011-2442-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation