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Comparative study on the chloroplast, mitochondrial and nuclear genome differentiation in two cultivated rice species, Oryza sativa and O. glaberrima, by RFLP analyses

Summary

Restriction fragment length polymorphisms of chloroplast (ct), mitochondrial (mt) and nuclear DNA were investigated using eight cultivars of Oryza sativa and two cultivars of O. glaberrima. Relative variability in the nuclear and cytoplasmic genomes was estimated by a common measure, genetic distance. Based on the average genetic distances among ten cultivars for each genome, the evolutionary variabilities of the mitochondrial and nuclear genomes were found to be almost the same, whereas the variability of the chloroplast genome was less than half that of the other two genomes. Cluster analyses on ct and mt DNA variations revealed that chloroplast and mitochondrial genomes were conservative within a taxon and that their differentiations were well-paralleled with respect to each other. For nuclear DNA variation, an array of different degrees of differentiation was observed in O. sativa, in contrast with little variation in O. glaberrima. As a whole, differentiation between O. sativa and O. glaberrima was clearly observed in all three genomes. In O. sativa, no notable difference was found between the cultivars ‘Japonica’ and ‘Javanica’, whereas a large differentiation was noticed between ‘Japonica’ (including ‘Javanica’) and ‘Indica’. In all three genomes, the average genetic distances within ‘Indica’ were much larger than those within ‘Japonica’ (including ‘Javanica’), and almost similar between ‘Japonica’ (including ‘Javanica’) and ‘Indica’. These facts indicate that differentiation in O. sativa was due mainly to ‘Indica’.

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References

  1. Dally AM, Second G (1990) Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, Section Oryza). Cladistic-mutation and genetic-distance analysis. Theor Appl Genet 80:209–222

    Google Scholar 

  2. Doebley J, Redfroe W, Blanton A (1987) Restriction site variation in the Zea chloroplast genome. Genetics 117:139–147

    Google Scholar 

  3. Hiratsuka J, Shimada H, Whittier R, 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

    Google Scholar 

  4. Ichikawa H, Hirai A, Katayama T (1986) Genetic analyses of Oryza species by molecular markers for chloroplast genomes. Theor Appl Genet 72:353–358

    Google Scholar 

  5. Ishii T, Terachi T, Tsunewaki K (1986) Restriction endonuclease analysis of chloroplast DNA from cultivated rice species, Oryza sativa and O. glaberrima. Jpn J Genet 61:537–541

    Google Scholar 

  6. Ishii T, Terachi T, Tsunewaki K (1988) Restriction endonuclease analysis of chloroplast DNA from A-genome diploid species of rice. Jpn J Genet 63:523–536

    Google Scholar 

  7. Kadowaki K, Yazaki K, Osumi T, Harada K, Katsuta M, Nakagahra M (1988) Distribution of mitochondrial plasmid-like DNA in cultivated rice (Oryza sativa L.) and its relationship with varietal groups. Theor Appl Genet 76:809–814

    Google Scholar 

  8. Kemble RJ, Gunn RE, Flavell RB (1980) Classification of normal and male-sterile cytoplasms in maize. II. Electrophoretic analysis of DNA species in mitochondria. Genetics 93:451–458

    Google Scholar 

  9. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

    Google Scholar 

  10. Mettler IJ (1987) A simple and rapid method for minipreparation of DNA from tissue cultured plant cells. Plant Mol Biol Rep 5:346–349

    Google Scholar 

  11. Morishima H, Hinata K, Oka HI (1963) Comparison of modes of evolution of cultivated forms from two wild rice species, Oryza breviligulata and O. perennis. Evolution 17:170–181

    Google Scholar 

  12. Neale DB, Wheeler NC, Allard RW (1986) Paternal inheritance of chloroplast DNA in Douglas-fir. Can J For Res 16:1152–1154

    Google Scholar 

  13. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  14. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    CAS  PubMed  Google Scholar 

  15. Ogihara Y, Tsunewaki K (1982) Molecular basis of the genetic diversity of the cytoplasm in Triticum and Aegilops. I. Diversity of the chloroplast genome and its lineage revealed by the restriction pattern of ctDNAs. Jpn J Genet 57:371–396

    Google Scholar 

  16. Ogihara Y, Tsunewaki K (1988) Diversity and evolution of chloroplast DNA in Triticum and Aegilops as revealed by restriction fragment analysis. Theor Appl Genet 76:321–332

    Google Scholar 

  17. Oka HI (1974) Experimental studies on the origin of cultivated rice. Genetics 78:475–486

    Google Scholar 

  18. Oka HI (1988) Origin of cultivated rice. Japan Scientific Societies Press, Tokyo/Elsevier, Amsterdam

    Google Scholar 

  19. Palmer JD, Shields CR, Cohen DB, Orton TJ (1983) Chloroplast DNA evolution and the origin of amphidiploid Brassica species. Theor Appl Genet 65:181–189

    Google Scholar 

  20. Pental D, Barnes SR (1985) Interrelationship of cultivated rice Oryza sativa and O. glaberrima with the wild O. perennis complex. Theor Appl Genet 70:185–191

    Google Scholar 

  21. Sederoff RR (1987) Molecular mechanisms of mitochondrial-genome evolution in higher plants. Am Nat 130:S35-S45

    Google Scholar 

  22. Sneath PHA, Sokal RR (1973) Numerical taxonomy. W. H. Freeman and Company, San Francisco

    Google Scholar 

  23. Song KM, Osborn TC, Williams PH (1988) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs). 1. Genome evolution of diploid and amphidiploid species. Theor Appl Genet 75:784–794

    CAS  Google Scholar 

  24. Takahashi N (1984) Differentiation of ecotypes in Oryza sativa L. In: Tsunoda S, Takahashi N (eds) Biology of rice. Japan Scientific Societies Press, Tokyo/Elsevier, Amsterdam, pp 31–67

    Google Scholar 

  25. Terachi T, Tsunewaki K (1986) The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops. 5. Mitochondrial genome diversity among Aegilops species having identical chloroplast genomes. Theor Appl Genet 73:175–181

    Google Scholar 

  26. Wang ZY, Tanksley SD (1989) Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113–1118

    Google Scholar 

  27. Watson JC, Thompson WF (1986) Purification and restriction endonuclease analysis of plant nuclear DNA. Methods Enzymol 118:57–75

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  29. Zhao X, Wu T, Xie Y, Wu R (1989) Genome-specific repetitive sequences in the genus Oryza. Theor Appl Genet 78:201–209

    Google Scholar 

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Correspondence to K. Tsunewaki.

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Communicated by G. Wenzel

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Ishii, T., Terachi, T., Mori, N. et al. Comparative study on the chloroplast, mitochondrial and nuclear genome differentiation in two cultivated rice species, Oryza sativa and O. glaberrima, by RFLP analyses. Theoret. Appl. Genetics 86, 88–96 (1993). https://doi.org/10.1007/BF00223812

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Key words

  • Cultivated rice species
  • Chloroplast DNA
  • Mitochondrial DNA
  • Nuclear DNA
  • RFLP analysis