Rice retroposon p-SINE1 and origin of cultivated rice

The wild rice species Oryza rufipogon displays wide intraspecific variations. It is considered to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. p-SINE1 is the first plant retroposon SINE identified in O. sativa and is present in strains of Oryza species with the AA genome in multiple copies. Some p-SINE1 members show interspecific insertion polymorphism among the rice strains and are thus assumed to be suitable markers for classifying the strains and to infer their relationships based in the presence or absence of the members at the corresponding loci. Subfamily members of p-SINE1 show insertion polymorphism in the O. sativa -O. rufipogon population. To determine the origin of cultivated rice, we used these p-SINE1 members to bar-code each of 101 cultivated and wild rice strains based on the insertion polymorphism at the respective loci. A phylogenetic tree constructed using the bar codes given to all the rice strains showed that O. sativa strains could be divided into two groups corresponding to japonica and indica, whereas O. rufipogon strains were divided into four groups, of which, one group consisted of annual O. rufipogon strains, while the other three of the perennial O. rufipogon strains. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains to the O. rufipogon annual strains, indicating that O. sativa had been derived. polyphyletically from O. rufipogon. Furthermore, we identified new p-SINE1 members showing interspecific insertion polymorphism from representative strains of four wild rice species with the AA genome, O. barthii, O. glumaepatula, O. longistaminata and O. meridionalis. A phylogenetic tree constructed using the polymorphic p-SINE1 members showed that O. longistaminata and O. meridionalis had diverged early, whereas the other species including O. rufipogon diverged relatively recently in an evolutionary time. We also presented the results of mapping of all p-SINE1 members identified from databases of rice genome sequences, and showed that they were present in all the chromosomes, but not distributed in the regions near the centromere in each chromosome, unlike other retroelements.