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Oryza officinalis complex includes five diploid species involving the B, C and E genomes, and is distributed in Asia, Africa and Oceania. These species are very important because O. australiensis is the only species with E genome, while O. punctata is the single species with B genome. Although there are three species with the C genome (O. eichinger...
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... O. rhizomatis (IRGC-103421) and O. eichingeri (IRGC-101429) possessed instead a SUB1 gene similar to the SUB1C-1 of domesticated submergence-tolerant indica rice ( Figure S11; Table 1). The C-genome group is a defined monophyletic clade (Ge et al., 1999), and phylogenetic and population genetic studies showed that the three closely related species belonging to this group, O. rhizomatis, O. eichingeri and Oryza officinalis, have diverged recently with a low level of species differentiation (Ge et al., 1999;Bao and Ge, 2003;Bao et al., 2006;Bautista et al., 2006). The absence of SUB1A in C-genome rice species is not surprising. ...
... O. rhizomatis (IRGC-103421) and O. eichingeri (IRGC-101429) possessed instead a SUB1 gene similar to the SUB1C-1 of domesticated submergence-tolerant indica rice ( Figure S11; Table 1). The C-genome group is a defined monophyletic clade (Ge et al., 1999), and phylogenetic and population genetic studies showed that the three closely related species belonging to this group, O. rhizomatis, O. eichingeri and Oryza officinalis, have diverged recently with a low level of species differentiation (Ge et al., 1999;Bao and Ge, 2003;Bao et al., 2006;Bautista et al., 2006). The absence of SUB1A in C-genome rice species is not surprising. ...
Crop tolerance to flooding is an important agronomic trait. Although rice (Oryza sativa) is considered a flood-tolerant crop, only limited cultivars display tolerance to prolonged submergence, which is largely attributed to the presence of the SUB1A gene. Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits. In this study, we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance. Oryza nivara and Oryza rufipogon accessions, belonging to the A-genome group, together with Oryza sativa, showed a wide range of submergence responses, and the tolerance-related SUB1A-1 and the intolerance-related SUB1A-2 alleles were found in tolerant and sensitive accessions, respectively. Flooding-tolerant accessions of Oryza rhizomatis and Oryza eichingeri, belonging to the C-genome group, were also identified. Interestingly, SUB1A was absent in these species, which possess a SUB1 orthologue with high similarity to O. sativa SUB1C. The expression patterns of submergence-induced genes in these rice genotypes indicated limited induction of anaerobic genes, with classical anaerobic proteins poorly induced in O. rhizomatis under submergence. The results indicated that SUB1A-1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C-genome group, which show instead a SUB1A-independent response to submergence.
... These results were consistent with previous reports [14,[21][22][23]. In the other clade, Cgenomes in different diploid species had differentiated apparently thereafter they partook in different polyploid formation (Figures 1, 2, 3), in agreement with other authors [58][59][60][61]. ...
Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process.
Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis.
C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids.
... The genus Oryza L. is agriculturally very important; it contains the famous crop rice, which is a staple food for 2.5 billion people in the world. As an important gene pool that can expand the genetic background of rice, the genus Oryza has been researched in detail on the basis of phylogenetics, genetic diversity, genomic reorganization, and resource conservation (Wang et al. 1992;Vaughan et al. 2003;Aggarwal et al. 1997Aggarwal et al. , 1999Ge et al. 1999Ge et al. , 2002Gao et al. 2001Gao et al. , 2002Gao et al. , 2005Xie et al. 2001;Bao and Ge 2003a;Bao et al. 2005;Zhou et al. 2003;Yoshida et al. 2004;Guo and Ge 2005). Recently, this genus has gained increasing interest, with a focus on polyploidy evolution (Ge et al. 1999;Bao and Ge 2004). ...
Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other
eukaryotes. Polyploidy induces genome-wide duplication. Studies on nucleotide diversity at homoeologous loci may provide insight
into the evolutionary dynamics of duplicate genes. In the present study, we estimated the levels and patterns of nucleotide
diversity for alcohol dehydrogenase 1 (adh1) loci in three American allotetraploid Oryza species: O. alta, O. grandiglumis, and O. latifolia. Higher nucleotide diversity was revealed in the C genome. This result suggested the different evolutionary dynamics of homoeologous
adh1 loci in these allotetraploid Oryza species.
... It is intriguing that the Sri Lankan O. eichinger is sympatric to O. rhizomatis with their population being overlapping in both northern and southern Sri Lanka, though their habitats are distinctly different (Bautista et al. 2006). Phylogenetic and population genetic studies showed that these 3 C-genome species have diverged recently with low level of species differentiation (Ge et al. 1999; Bao and Ge 2003; Bao et al. 2006; Bautista et al. 2006 ). Therefore, O. officinalis and its close relatives provide an ideal system to explore demographic history and speciation processes in plants. ...
... Four O. rhizomatis individuals were sampled to represent the species that is found only in Sri Lanka. Because our previous studies found high level of genetic divergence between the African and Sri Lankan populations of O. eichingeri (Bao and Ge 2003; Bao et al. 2006 ), we treated this species as 2 geographic races and sampled 4 individuals from each of them. Additionally, 3 accessions of the diploid Oryza punctata, a B-genome species, were sampled as outgroups because previous studies showed that the B-genome species was closely related to the C-genome group (Ge et al. 1999). ...
... Oryza officinalis and O. rhizomatis can be differentiated from O. eichingeri in that the former 2 have rhizomes (Vaughan 1990 ). Compared with O. rhizomatis, O. officinalis has smaller spikelets, shorter palea tip, and more approximately equal branches from the lowest panicle node. Morphologically, O. officinalis is more similar to O. rhizomatis than to O. eichingeri (Vaughan 1990 ), which was supported by phylogenetic analysis based on multiple gene sequences (Bao and Ge 2003). In contrast, recent AFLP (Bautista et al. 2006) and SSR (Bao et al. 2006) analyses suggested that O. rhizomatis was more genetically similar to O. eichingeri than to O. officinalis. ...
Nucleotide variation in 10 unlinked nuclear genes was investigated in species-wide samples of Oryza officinalis and its close relatives (Oryza eichingeri and Oryza rhizomatis). Average estimates of nucleotide diversity were the lowest in O. rhizomatis ((sil) = 0.0038) and the highest in O. eichingeri ((sil) = 0.0057) that is disjunctly distributed in Africa and Sri Lanka. These wild rice species appeared to harbor relatively low levels of nucleotide variation relative to other plant species because the diversity level of O. eichingeri is only 23-46% of those in Zea species and 35% of that in Arabidopsis thaliana. The lower nucleotide diversity in these Oryza species could be best explained by their smaller historic effective population sizes. The speciation model test indicated that O. officinalis and its close relatives might have undergone a process of population contraction since divergence from their ancestor. Incongruent topologies among 10 gene trees, particularly regarding the positions of O. eichingeri and O. rhizomatis accessions might be attributed to lineage sorting arising from ancient polymorphism and hybridization/introgression between the Sri Lankan O. eichingeri and O. rhizomatis. However, the null hypothesis of the isolation model was not rejected for any contrast between taxa, which suggested that no subsequent gene flow shaped the present patterns of nucleotide variation since their divergence and that introgression was not pervasive in this group of species. Our molecular dating provides an approximate divergence time of 0.37 Myr between 2 geographical races of O. eichingeri, much more recent compared with the times of other speciation events in this group (0.63-0.68 Myr). A long-distance dispersal from West Africa to Sri Lanka was more likely to play a role in the disjunct distribution of O. eichingeri.
... In their phenogram developed based on sequences of a gypsy-like retrotransposon, Shcherban et al. (2001) found that O. eichingeri from two continents fell into different clusters, and suggested that O. eichingeri was more closely related to the ancestral species of the complex. RFLP analysis (Federici et al., 2002) and mukigene phylogenetic study (Bao and Ge, 2003) also detected high degree of differentiation between the two geographical races. In fact, the taxonomic status of O. eichingeri confined to Sri Lanka has been a subject of controversy (Bor, 1960;Tateoka, 1962;Nayar, 1973;Vaughan, 1990). ...
Genetic diversity and evolutionary relationships of 72 accessions representing six species with the B-, C-, and BC-genomes
in the genusOryza were investigated by seven microsatellite markers. Of four diploid species,Oryza officinalis maintained the highest diversity (P=71.4%, He=0.565), followed by Oryza eichingeri (P=57.1%, He=0.376), Oryzapunctata (P=57.1%, He=0.272) and Oryza rhizomatis (P=42.9%, He=0.222). In comparison, a higher level of genetic diversity was revealed
in the tetraploid (P=71.4%, He=0.461-0.637). UPGMA dendrograms based on genetic distance revealed an obvious genetic differentiation
between Asian and African races ofO. eichingeri. Three BBCC species clustered with different accessions of the diploidO. punctata, suggestive of their multiple origins. The results inferred from the dendrogram suggested that diploid species,O. officinalis and AfricanO. eichingeri might be the C-genome donors for tetraploid species,Oryza minuta andO. punctata, respectively, while the C-genome ancestor ofOryza malampuzhaensis seemed to be eitherO. rhizomatis or the Sri LankanO. eichingeri species. The genetic relationship among the CC and BBCC species further indicated that the tetraploid species with the BC-genome
have originated independently, at least three times in history. In addition, we have demonstrated successful cross-species
amplification of seven rice SSR loci acrossOryza species with B-and C-genomes.
KeywordsB- and C-genome-evolutionary relationships-genetic diversity-microsatellite-
Oryza
... Importance has been attached to the genetic diversity of chloroplast DNA (cpDNA) of rice, as rice is one of the most important crops in the world and the function of chloroplast, where plant photosynthesis takes place, is a crucial factor for fully increasing heterosis potential. The research results on rice cpDNA at the nucleotide level using microsatellites, ORF(open reading frame)100 or mat K (maturase K) gene as markers show that there is a certain rich genetic diversity in genes, ORFs or spacers (Provan et al.1996; Bao and Ge 2003; Prathepha and Baimai 2004; Nishikawa et al. 2005). And the diversity in cultivated indica rice is the richest (Garris et al. 2005). ...
The ORF100, ORF29-TrnC(GCA) spacer, rps16 gene intron and TrnT(UGU)-TrnL(UAA) spacer of chloroplast DNA (cpDNA) of 6 photoperiod-sensitive genic male sterile (PGMS) rice, Nongken58S and its 5 derivatives, were amplified and sequenced. According to the result of ORF100 and ORF29-TrnC(GCA) spacer analysis, the cpDNA of japonica PGMS line Nongken58S was Japonica, and among those PGMS lines derived from Nongken58S, cpDNA of japonica 7001S and 3 indica lines 1103S, Peiai64S and Guangzhan63S were that of japonica, which was in accordance with the cytoplasm pedigree provided by their breeders. But the cpDNA of indica PGMS line W6154S was that of indica, which disaccorded with the cytoplasm pedigree, so we conjectured that the breeders had used the PGMS line as the male parent. Basing on the result of sequence analysis, we found single nucleotide polymorphism in rps16 gene intron and TrnT(UGU)-TrnL(UAA) spacer of these 5 japonica PGMS lines.
... The molecular work on Oryza has been carried out by Dr. S. Ge (PE) and his fellow Bao, and Ge 2003), and another taxon has also been reported recently (Saarela et al. 2003). ...
... In the past few years, molecular work has dominated most of Chinese systematic works, and published either in China Ehrendorfer and Samuel 2001;Hong et al. 2001;Bao and Ge 2003;Wang WP et al. 2003) or abroad (Shi et al. 2001;Song et al. 2001;Kong et al. 2002a,b;). More and more Chinese scholars submitted their papers worldwide. ...
