Molecular Genetics and Genomics

, Volume 272, Issue 5, pp 504–511

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

Original Paper

Abstract

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.

Keywords

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

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)

References

  1. Audley-Charles MG, Hurley AM, Smith AG (1981) Continental movements in the mesozoic and cenozoic. In: Whitmore TC (ed) Wallace’s line and plate tectonics. Clarendon Press, Oxford, UK, pp 9–23Google Scholar
  2. Blair MW, Panaud O, McCouch SR (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.) Theor Appl Genet 98:780–782Google Scholar
  3. Chang TT (1976) The origin, evolution, cultivation, dissemination and diversification of Asian and African rices. Euphytica 25:435–485Google Scholar
  4. Chen B (1999) Origin of 8000-year-old cultivated rice in Henan’s Jia Lake site. Agric Archaeol 1:55–57Google Scholar
  5. Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75CrossRefPubMedGoogle Scholar
  6. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079CrossRefPubMedGoogle Scholar
  7. Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–50CrossRefPubMedGoogle Scholar
  8. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93:10274–10279CrossRefPubMedGoogle Scholar
  9. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30Google Scholar
  10. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR (2002) A recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161:1293–1305PubMedGoogle Scholar
  11. Kato S, Kosaka H, Hara S (1928) On the affinity of the cultivated varieties of rice plants, Oryza sativa L. Bull Sci Fac Agric Kyushu Univ, Fukuoka, Japan 3:132Google Scholar
  12. Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34CrossRefPubMedGoogle Scholar
  13. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532CrossRefPubMedGoogle Scholar
  14. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedGoogle Scholar
  15. Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E (1999) Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol Gen Genet 260:593–602CrossRefPubMedGoogle Scholar
  16. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14:860–869CrossRefPubMedGoogle Scholar
  17. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426PubMedGoogle Scholar
  18. Oka HI, Chang TT (1962) Rice varieties intermediate between wild and cultivated forms and the origin of the Japonica type. Bot Bull Acad Sinica 3:109–131Google Scholar
  19. Oka H, Morishima H (1997) Wild and cultivated rice. In: Matsuo T, Futsuhara Y, Kikushi F, Yamaguchi H (eds) Science of the rice plant (vol 3: Genetics). Nobunkyo, Tokyo, pp 88–111Google Scholar
  20. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607CrossRefPubMedGoogle Scholar
  21. Panaud O, Vitte C, Hivert J, Muzlak S, Talag J, Brar DS, Sarr A (2002) Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis. Mol Genet Genomics 268:113–121CrossRefPubMedGoogle Scholar
  22. Petrov D, Lozovskaya E, Hartl D (1996) High intrinsic rate of DNA loss in Drosophila. Nature 384:346–349CrossRefPubMedGoogle Scholar
  23. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45CrossRefPubMedGoogle Scholar
  24. Second G (1982) Origin of the genetic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57Google Scholar
  25. Wang ZY, Tanksley SD (1989) Restriction fragment length polymorphism in Oryza sativa L.. Genome 32:1113–1118Google Scholar
  26. Yu J, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science 296:79–92CrossRefPubMedGoogle Scholar

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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