Molecular Genetics and Genomics

, Volume 272, Issue 5, pp 504–511 | Cite as

Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.)

  • C. Vitte
  • T. Ishii
  • F. Lamy
  • D. Brar
  • O. Panaud
Original Paper


The origin of rice domestication has been the subject of debate for several decades. We have compared the transpositional history of 110 LTR retrotransposons in the genomes of two rice varieties, Nipponbare (Japonica type) and 93-11 (Indica type) whose complete sequences have recently been released. Using a genomic paleontology approach, we estimate that these two genomes diverged from one another at least 200,000 years ago, i.e., at a time which is clearly older than the date of domestication of the crop (10,000 years ago, during the late Neolithic). In addition, we complement and confirm this first in silico analysis with a survey of insertion polymorphisms in a wide range of traditional rice varieties of both Indica and Japonica types. These experimental data provide additional evidence for the proposal that Indica and Japonica rice arose from two independent domestication events in Asia.


LTR-retrotransposons Rice Domestication Indica/Japonica Retrotransposon-Based Insertion Polymorphism (RBIP) 



The authors thank A. Frary for her helpful comments on the manuscript and S. Yanagihara for his valuable help in choosing the traditional Japonica varieties used for the analysis.

Supplementary material

Suppl. Data #1 Description of the 110 insertions of LTR retroelements used in the study

supp1.pdf (22 kb)
(PDF 23 KB)

Suppl. Data #2 Description of the 13 insertions for which the PCR assay has been performed

supp2.pdf (8 kb)
(PDF 9 KB)

Suppl. Data #3 Germplasm information

supp3.pdf (11 kb)
(PDF 11 KB)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • C. Vitte
    • 1
  • T. Ishii
    • 2
  • F. Lamy
    • 1
  • D. Brar
    • 3
  • O. Panaud
    • 4
  1. 1.Laboratoire Ecologie Systematique et EvolutionUniversité Paris-SudOrsay CedexFrance
  2. 2.Laboratory of Plant Breeding, Faculty of AgricultureKobe UniversityKobeJapan
  3. 3.Plant Breeding Genetics and Biochemistry DivisionInternational Rice Research InstituteMetro ManilaPhilippines
  4. 4.Laboratoire Genome et Developpement des PlantesUniversité de PerpignanPerpignan CedexFrance

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