Theoretical and Applied Genetics

, Volume 81, Issue 5, pp 693–702 | Cite as

Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing

  • P. Barbier
  • H. Morishima
  • A. Ishihama


The phylogenetic relationships between Asian wild rice strains were analyzed by direct sequencing of PCR-amplified DNA fragments. The sequence of three introns located in the phytochrome gene was determined for eight strains of the Asian wild rice, Oryza rufipogon, and one strain of the related African species, Oryza longistaminata. The number of nucleotide substitutions per site between various strains within a single species, O. rufipogon, ranged between 0.0017 and 0.0050, while those between two related species, O. rufipogon and O. longistaminate, were 0.043–0.049 (23–26 within 532 bp). Taken together with the sequence differences of the 10-kDa prolamin gene, a model is proposed for the phylogenetic relationships and evolutionary history of annuals and perennials within O. rufipogon.

Key words

Asian wild rice Phytochrome intron Polymerase chain reaction (PCR) Direct DNA sequencing Intraspecific DNA polymorphism 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Aquadro CF, Lado KM, Moon WA (1988) The rosy region of D. melanogaster and D. simulans: contrasting levels of naturally occurring DNA restriction map variation and divergence. Genetics 119:875–888Google Scholar
  2. Barbier P (1987) Ecological genetic study on wild rice populations from Thailand. MS thesis, Nagoya University, JapanGoogle Scholar
  3. Barbier P (1989) Genetic variation and ecotypic differentiation in the wild rice Oryza rufipogon. I. Population differentiation in life-history traits and isozymes. Jpn J Genet 64:259–271Google Scholar
  4. Barbier P (1990) The annual-perennial differentiation in wild rice: quantitative and molecular genetic studies. PhD thesis, Nagoya University, JapanGoogle Scholar
  5. Barbier P, Ishihama A (1990) Variation in the nucleotide sequence of a prolamin gene family in wild rice. Plant Mol Biol 15:191–195Google Scholar
  6. Carothers AM, Urlaub G, Mucha J, Grunberger D, Chasin LA (1989) Point mutation analysis in a mammalian gene: rapid preparation of total DNA, PCR amplification of cDNA and Taq sequencing by a novel method. Biotechniques 7:494–499Google Scholar
  7. Clegg MT (1989) Molecular diversity in plant populations. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Sinauer, Sunderland/MA, pp 98–115Google Scholar
  8. Cordesse F, Second G, Delseny M (1990) Ribosomal gene spacer length variability in cultivated and wild rice species. Theor Appl Genet 79:81–88Google Scholar
  9. Dally A (1988) Polymorphisme des longueurs des fragments de restriction de l'ADN chloroplastique dans la section Eu Oryza du genre Oryza et implications phylogenetiques. PhD thesis, Université des Sciences et Techniques du Languedoc, FranceGoogle Scholar
  10. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA preparation, version II. Plant Mol Biol Rep 1[4]:19–21Google Scholar
  11. Gepts P, Clegg MT (1989) Genetic diversity in pearl millet [Pennisetum glaucum (L.) R.Br.] at the DNA sequence level. J Hered 80:203–208Google Scholar
  12. Ishii T, Terachi T, Tsunewaki K (1989) Restriction endonuclease analysis of chloroplast DNA from A-genome diploid species of rice. Jpn J Genet 72:353–358Google Scholar
  13. Johns MA, Strommer JN, Freeling M (1983) Exceptionally high levels of restriction site polymorphism in DNA near the maize Adh-1 gene. Genetics 105:733–743Google Scholar
  14. Kay SA, Keith B, Shinozaki K, Chua N-H (1989a) The sequence of the rice phytochrome gene. Nucleic Acids Res 17:2865–2866Google Scholar
  15. Kay SA, Keith B, Shinozaki K, Chye ML, Chua NH (1989b) The rice phytochrome gene: autoregulated expression and binding of GT-1 to a conserved site in the 5′ upstream region. Plant Cell 1:351–360Google Scholar
  16. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120Google Scholar
  17. Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304:412–417Google Scholar
  18. Langley CH, Aquadro CF (1987) Restriction map variation in natural populations of D. melanogaster. Mol Biol Evol 4:651–663Google Scholar
  19. Langley CH, Shimpton AE, Yamazaki T, Miyashita N, Matsuo Y, Aquadro CF (1988) Naturally occurring variation in the restriction map of the Amy region of D. melanogaster. Genetics 119:619–629Google Scholar
  20. Law R, Bradshaw AD, Putwain PD (1977) Life-history variation in Poa annua. Evolution 31:233–246Google Scholar
  21. Li WH, Luo CC, Wu CI (1985) Evolution of DNA sequences. In: MacIntyre RC (ed) Molecular evolutionary genetics. Plenum, New York, pp 1–93Google Scholar
  22. Mettler IJ (1985) A simple and rapid method for minipreparation of DNA from tissue-cultured plant cells. Plant Mol Biol Rep 5:346–349Google Scholar
  23. Morishima H, Oka HI (1970) A survey of genetic variations in the populations of wild Oryza species and their cultivated relatives. Jpn J Genet 45:371–385Google Scholar
  24. Morishima H, Sano Y, Oka HI (1984) Differentiation of perennial and annual types due to habitat conditions in the wild rice Oryza perennis. Plant Syst Evol 144:119–135Google Scholar
  25. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  26. Oka HI (1988) In: Origin of cultivated rice. Elsevier, Amsterdam, pp 18–22Google Scholar
  27. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/NYGoogle Scholar
  28. Sano Y, Sano R (1990) Variation in the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33:209–218Google Scholar
  29. Sano Y, Morishima H, Oka HI (1980) Intermediate perennial-annual populations of Oryza perennis found in Thailand and their evolutionary significance. Bot Mag Tokyo 93:291–305Google Scholar
  30. Second G (1985) Evolutionary relationships in the sativa group of Oryza based on isozyme data. Genet Sel Evol 17:89–114Google Scholar
  31. Snedecor GW (1957) Statistical methods. Iowa State College Press, AmesGoogle Scholar
  32. Stephens JC, Nei M (1985) Phylogenetic analysis of polymorphic DNA sequences at the Adh locus in Drosophila melanogaster and its sibling species. J Mol Evol 22:289–300Google Scholar
  33. Venable DL (1984) Using intraspecific variation to study the ecological significance and evolution of plant life-histories. In: Dirzo R, Sarukhan J (eds) Perspectives on plant population ecology. Sinauer, Sunderland/MA, pp 166–187Google Scholar
  34. Whyte RO (1972) The gramineae, wild and cultivated, of monsoonal and equatorial Asia. Asian Perspect 15:127–151Google Scholar
  35. Wilson AC, Zimmer EA, Prager EM, Kocher TD (1989) In: Fermholm B, Bremer K, Jornvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 407–419Google Scholar
  36. Wolfe KH, Li WH, Sharp PH (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplastic, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058Google Scholar
  37. Wolfe KH, Sharp PM, Li WH (1989) Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29:208–211Google Scholar

Copyright information

© Springer-Verlag 1991

Authors and Affiliations

  • P. Barbier
    • 1
    • 2
  • H. Morishima
    • 2
  • A. Ishihama
    • 1
  1. 1.Department of Molecular GeneticsNational Institute of GeneticsShizuokoJapan
  2. 2.Department of Agricultural GeneticsNational Institute of GeneticsShizuokoJapan

Personalised recommendations