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Mol. Biol. Evol. 20(1):67-75. 2003
DOI: 10.1093/molbev/msg004
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Polyphyletic Origin of Cultivated Rice: Based on the Interspersion Pattern of SINEs

Chaoyang Cheng*, Reiko Motohashi*,1, Suguru Tsuchimoto*, Yoshimichi Fukuta{dagger}, Hisako Ohtsubo* and Eiichi Ohtsubo*

* Institute of Molecular and Cellular Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
{dagger} Hokuriku National Agricultural Experimental Station, Joetsu, Japan

The wild rice species Oryza rufipogon with wide intraspecific variation is thought to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. To determine the origin of cultivated rice, subfamily members of the rice retroposon p-SINE1, which show insertion polymorphism in the O. sativa –O. rufipogon population, were identified and used to "bar code" each of 101 cultivated and wild rice strains based on the presence or absence of the p-SINE1 members at the respective loci. A phylogenetic tree constructed based on the bar codes given to the rice strains showed that O. sativa strains were classified into two groups corresponding to japonica and indica, whereas O. rufipogon strains were in four groups, in which annual O. rufipogon strains formed a single group, differing from the perennial O. rufipogon strains of the other three groups. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains were closely related to the O. rufipogon annual strains, indicating that O. sativa has been derived polyphyletically from O. rufipogon. The subfamily members of p-SINE1 constitute a powerful tool for studying the classification and relationship of rice strains, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains.

Key Words: Oryza sativa • indica and japonica rice • Oryza rufipogon • SINE • insertion polymorphism • polyphyletic origin


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