Evolutionary relationships among rice species with AA genome based on SINE insertion analysis.

Abstract

Previous studies based on morphological and molecular markers indicated that there are two cultivated and five wild rice species within the Oryza genus with the AA genome. In the cultivated rice species, Oryza sativa , a retroposon named p-SINE1 has been identified. Some of the p-SINE1 members characterized previously showed interspecific insertion polymorphisms in the species with the AA genome. In this study, we identified new p-SINE1 members showing interspecific insertion polymorphisms from representative strains of four wild rice species with the AA genome: O. barthii , O. glumaepatula , O. longistaminata , and O. meridionalis . Some of these members were present only in strains of one species, whereas the others were present in strains of two or more species. The p-SINE1 insertion patterns in the strains of the Asian and African cultivated rice species O. sativa and O. glaberrima were very similar to those of the Asian and African wild rice species O. rufipogon and O. barthii , respectively. This is consistent with the previous hypothesis that O. sativa and O. glaberrima are derived from specific wild rice species. Phylogenetic analysis based on the p-SINE1 insertion patterns showed that the strains of each of the five wild rice species formed a cluster. The strains of O. longistaminata appear to be distantly related to those of O. meridionalis . The strains of these two species appear to be distantly related to those of three other species, O. rufipogon , O. barthii and O. glumaepatula . The latter three species are closely related to one another with O. barthii and O. glumaepatula being most closely related. A phylogenetic tree including a hypothetical ancestor with all loci empty for p-SINE1 insertion showed that the strains of O. longistaminata are related most closely to the hypothetical ancestor. This indicates that O. longistaminata and O. meridionalis diverged early on, whereas the other species diverged relatively recently, and suggests that the Oryza genus with AA genome might have originated in Africa, rather than in Asia.

DNA polymorphism in the blast disease resistance gene Pita of the wild rice Oryza rufipogon and its related species

“…The Pita sequences of O. meridionalis were determined by two independent sequencing experiments. The present findings were inconsistent with a prior phylogenetic tree based not only on sequence variations in Adh1 and Adh2 (Yoshida et al, 2004;Yoshida and Miyashita, 2005), but also on RFLP, RAPD (Ishii et al, 1996;Bautista et al, 2001), and SINE insertion polymorphisms (Cheng et al, 2002), which sug- (Supplementary fig. 2).…”

“…Sequence type B could be corresponding to the H-OB. The H-OB O. rufipogon accessions tested by Huang et al (2008) (Ishii et al, 1996;Bautista et al, 2001;Cheng et al, 2002). Therefore, the direction of the introgression is not clear in our data.…”

The wild Oryza collection in National BioResource Project (NBRP) of Japan: History, biodiversity and utility

“…Short interspersed elements (SINEs) of retroposons have also been used for phylogenetic studies, because a single SINE copy, once inserted, remains in the genomic locus. Cheng et al (2002) identified p-SINE1 in the O. sativa genome, and showed that it is a powerful tool for classification of cultivated and wild rice species. Another wild rice accession of O. rufipogon repeatedly used by international teams for QTL studies (IRGC 105491) is originally NIG W0574 collected in 1959 in Malaysia.…”

Mitochondrial gene in the nuclear genome induces reproductive barrier in rice

“…This indicates that the segmental genomic duplication carrying mtRPL27 at S27 occurred before the divergence of the rice AA genome species and that the duplicated segments at S27 spread in each species, except O. glumaepatula, which is the sole South American species possessing the AA genome and is thought to have an African origin (29). Indeed, the O. glumaepatula accessions used in this study were closely related to the O. barthii and O. glaberrima complex (28,30,31) (also see Fig. S6).…”