Summary
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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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 119:875–888
Barbier P (1987) Ecological genetic study on wild rice populations from Thailand. MS thesis, Nagoya University, Japan
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 64:259–271
Barbier P (1990) The annual-perennial differentiation in wild rice: quantitative and molecular genetic studies. PhD thesis, Nagoya University, Japan
Barbier P, Ishihama A (1990) Variation in the nucleotide sequence of a prolamin gene family in wild rice. Plant Mol Biol 15:191–195
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 7:494–499
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 98–115
Cordesse F, Second G, Delseny M (1990) Ribosomal gene spacer length variability in cultivated and wild rice species. Theor Appl Genet 79:81–88
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, France
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA preparation, version II. Plant Mol Biol Rep 1[4]:19–21
Gepts P, Clegg MT (1989) Genetic diversity in pearl millet [Pennisetum glaucum (L.) R.Br.] at the DNA sequence level. J Hered 80:203–208
Ishii T, Terachi T, Tsunewaki K (1989) Restriction endonuclease analysis of chloroplast DNA from A-genome diploid species of rice. Jpn J Genet 72:353–358
Johns MA, Strommer JN, Freeling M (1983) Exceptionally high levels of restriction site polymorphism in DNA near the maize Adh-1 gene. Genetics 105:733–743
Kay SA, Keith B, Shinozaki K, Chua N-H (1989a) The sequence of the rice phytochrome gene. Nucleic Acids Res 17:2865–2866
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 1:351–360
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304:412–417
Langley CH, Aquadro CF (1987) Restriction map variation in natural populations of D. melanogaster. Mol Biol Evol 4:651–663
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 119:619–629
Law R, Bradshaw AD, Putwain PD (1977) Life-history variation in Poa annua. Evolution 31:233–246
Li WH, Luo CC, Wu CI (1985) Evolution of DNA sequences. In: MacIntyre RC (ed) Molecular evolutionary genetics. Plenum, New York, pp 1–93
Mettler IJ (1985) A simple and rapid method for minipreparation of DNA from tissue-cultured plant cells. Plant Mol Biol Rep 5:346–349
Morishima H, Oka HI (1970) A survey of genetic variations in the populations of wild Oryza species and their cultivated relatives. Jpn J Genet 45:371–385
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 144:119–135
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Oka HI (1988) In: Origin of cultivated rice. Elsevier, Amsterdam, pp 18–22
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/NY
Sano Y, Sano R (1990) Variation in the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33:209–218
Sano Y, Morishima H, Oka HI (1980) Intermediate perennial-annual populations of Oryza perennis found in Thailand and their evolutionary significance. Bot Mag Tokyo 93:291–305
Second G (1985) Evolutionary relationships in the sativa group of Oryza based on isozyme data. Genet Sel Evol 17:89–114
Snedecor GW (1957) Statistical methods. Iowa State College Press, Ames
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 22:289–300
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 166–187
Whyte RO (1972) The gramineae, wild and cultivated, of monsoonal and equatorial Asia. Asian Perspect 15:127–151
Wilson AC, Zimmer EA, Prager EM, Kocher TD (1989) In: Fermholm B, Bremer K, Jornvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 407–419
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 84:9054–9058
Wolfe KH, Sharp PM, Li WH (1989) Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29:208–211
Author information
Authors and Affiliations
Additional information
Communicated by K. Tsunewaki
Rights and permissions
About this article
Cite this article
Barbier, P., Morishima, H. & Ishihama, A. Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing. Theoret. Appl. Genetics 81, 693–702 (1991). https://doi.org/10.1007/BF00226739
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00226739