Theoretical and Applied Genetics

, Volume 114, Issue 4, pp 731–743 | Cite as

Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice

  • Sujay Rakshit
  • Arunita Rakshit
  • Hideo Matsumura
  • Yoshihiro Takahashi
  • Yoshitaka Hasegawa
  • Akiko Ito
  • Takashige Ishii
  • Naohiko T. Miyashita
  • Ryohei TerauchiEmail author
Original Paper


Polymorphism over ∼26 kb of DNA sequence spanning 22 loci and one region distributed on chromosomes 1, 2, 3 and 4 was studied in 30 accessions of cultivated rice, Oryza sativa, and its wild relatives. Phylogenetic analysis using all the DNA sequences suggested that O. sativa ssp. indica and ssp. japonica were independently domesticated from a wild species O. rufipogon. O. sativa ssp. indica contained substantial genetic diversity (π = 0.0024), whereas ssp. japonica exhibited extremely low nucleotide diversity (π = 0.0001) suggesting the origin of the latter from a small number of founders. O. sativa ssp. japonica contained a larger number of derived and fixed non-synonymous substitutions as compared to ssp. indica. Nucleotide diversity and genealogical history substantially varied across the 22 loci. A locus, RLD15 on chromosome 2, showed a distinct genealogy with ssp. japonica sequences distantly separated from those of O. rufipogon and O. sativa ssp. indica. Linkage disequilibrium (LD) was analyzed in two different regions. LD in O. rufipogon decays within 5 kb, whereas it extends to ∼50 kb in O. sativa ssp. indica.


Linkage Disequilibrium Significant Linkage Disequilibrium African Species Oryza Species Relative Rate Test 
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.



SR conducted this work under financial support from Japanese Society for Promotion of Sciences, Tokyo. RT thanks B. Till, L. Comai and S. Henikoff, Washington University, Seatle, USA for training him with TILLING technique. We thank N. Kurata, National Institute of Genetics, Mishima, Japan for providing rice seeds, and J. Rozas, University of Barcelona, Spain for guiding us with the DnaSP program, two anonymous reviewers and M. Morgante, University of Udine, Italy for valuable comments to the earlier version of the manuscript. This work was supported by the “Program for Promotion of Basic Research Activities for Innovative Biosciences” (Japan), “Iwate University 21st Century COE Program: Establishment of Thermo-Biosystem Research Program” and “JSPS grant no. 18310136” to RT.

Supplementary material


Supplementary Fig. 1. Results of multilocus HKA test. Contributions to the overall χ2 test static by the polymorphism and divergence observations for each locus. Squares indicate divergence between African and Asian species, and circles correspond to polymorphism within Asian species. If the observed value was greater than the expected, then the point is placed above the line; otherwise it is placed below the line (JPG 74 kb)

122_2006_473_MOESM1_ESM.doc (50 kb)
Supplementary Table 1. Plant materials used in the LD study (DOC 51 kb)
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Supplementary Table 2. Summary of 22 loci studied (DOC 25 kb)
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Supplementary Table 3. DNA polymorphism of O. sativa and O. rufipogon for silent positions (non-coding and coding synonymous sites) at the 22 loci (DOC 34 kb)
122_2006_473_MOESM4_ESM.doc (32 kb)
Supplementary Table 4. Contrasting levels of synonymous and replacement variation (DOC 33 kb)
122_2006_473_MOESM5_ESM.doc (25 kb)
Supplementary Table 5. Number of segregating sites within all positions (coding and non-coding positions) for Asian Oryza species (DOC 25 kb)
122_2006_473_MOESM6_ESM.doc (30 kb)
Supplementary Table 6. DNA variation in RLD15 locus (Only non-singleton mutations are shown. There were 67 singleton mutations specific to O. australiensis) (DOC 30 kb)
122_2006_473_MOESM7_ESM.doc (32 kb)
Supplementary Table 7. Shared polymorphism and fixed differences among O. sativa ssp. indica, ssp. japonica and O. rufipogon (DOC 33 kb)
122_2006_473_MOESM8a_ESM.xls (23 kb)
Supplementary Table 8a. LD in O. rufipogon (XLS 23 kb)
122_2006_473_MOESM8b_ESM.xls (23 kb)
Supplementary Table 8b. LD in O. sativa (XLS 23 kb)
122_2006_473_MOESM8c_ESM.xls (24 kb)
Supplementary Table 8c. LD in O. sativa ssp. indica (XLS 24 kb)
122_2006_473_MOESM8d_ESM.xls (26 kb)
Supplementary Table 8d. LD in O. sativa ssp. japonica (XLS 26 kb)


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Sujay Rakshit
    • 1
    • 2
  • Arunita Rakshit
    • 1
  • Hideo Matsumura
    • 1
  • Yoshihiro Takahashi
    • 1
  • Yoshitaka Hasegawa
    • 1
  • Akiko Ito
    • 1
  • Takashige Ishii
    • 3
  • Naohiko T. Miyashita
    • 4
  • Ryohei Terauchi
    • 1
    • 5
    Email author
  1. 1.Iwate Biotechnology Research CenterKitakamiJapan
  2. 2.Indian Agricultural Research Institute, PusaNew DelhiIndia
  3. 3.Laboratory of Plant Breeding, Faculty of AgricultureKobe UniversityKobeJapan
  4. 4.Laboratory of Plant Genetics, Graduate School of AgricultureKyoto UniversityKyotoJapan
  5. 5.The United Graduate School of Agricultural SciencesIwate UniversityIwateJapan

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