Rice Retroposon p-SINE1 and Origin of Cultivated Rice

Abstract

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 on 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.

Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs

“…In the paper of Morishima et al (1984), it was suggested that the intermediate plants are ecologically unstable and when disruptive selection is strong enough, they can be differentiated into perennial and annual types. Mochizuki et al, 1992;Motohashi et al, 1997;Cheng et al, 2002;Ohtsubo et al, 2004). There are 112 RA-subfamily members, including 64 RAα and 18 RAβ members.…”

Two new SINE elements, p-SINE2 and p-SINE3, from rice

“…In a similar manner to the p-SINE1 members, the p-SINE2 and p-SINE3 members appear to be dispersed randomly along each of the 12 chromosomes ( Fig. 5; Ohtsubo et al, 2004), but unlike other retrotransposons and autonomous transposable elements that form a cluster in the heterochromatin of pericentromeric regions (Sasaki et al, 2002;Feng et al, 2002; The Rice Chromosome 10 Sequencing Consortium 2003). Of 17 p-SINE2 members, 10 were present in the putative or hypothetical exons or introns, or within a 0.5 kb region of genes or the putative coding regions (Table 1).…”

“…1), was identified in the introns of the Waxy gene in O. sativa (Umeda et al, 1991), and since then a large number of p-SINE1 members have been identified from rice species in the O. sativa and O. officinalis complexes (Mochizuki et al, 1993;Motohashi et al, 1997;Cheng et al, 2002Cheng et al, , 2003Xu, 2004). These include members of the RA (Recently Amplified) subfamily that consists of two groups, RA α and RA β (see Ohtsubo et al, 2004), most of which show insertion polymorphisms within O. sativa and its ancestral wild species O. rufipogon with the AA genome. The presence or absence of these polymorphic members has been used for phylogenetic analysis of strains in these species (Cheng et al, 2003;also Xu, 2004).…”

Analysis of distribution and proliferation of mPing family transposons in a wild rice (Oryza rufipogon Griff.)

“…All O. rufipogon accessions used in this study were selected from core collection rank 1, 2, and 3, because these collection covered typical species-specific phenotypes and wide distribution in the habitat. AA genome species in the core collections are distinguished by SINE code which is the criteria of species based on the presence or absence of retrotransposon p-SINE insertions (Ohtsubo et al 2004). The genomic constitution, species name, habitat and SINE code of each accession are presented in Table 1.…”