Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.)
- 547 Downloads
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.
KeywordsLTR-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.
- 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
- 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
- Chang TT (1976) The origin, evolution, cultivation, dissemination and diversification of Asian and African rices. Euphytica 25:435–485Google Scholar
- Chen B (1999) Origin of 8000-year-old cultivated rice in Henan’s Jia Lake site. Agric Archaeol 1:55–57Google Scholar
- Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30Google Scholar
- 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
- 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
- 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
- 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
- Wang ZY, Tanksley SD (1989) Restriction fragment length polymorphism in Oryza sativa L.. Genome 32:1113–1118Google Scholar