Comparative Analysis Of Oryza Genomes By Repetitive Sequences

In this paper, several wild rice species were used as research materials, including O. punctata, O. brachyantha, O. officinalis, O. australiensis, O. schweinfurthiana, O. alta, O. latifolia, and tow cultivated species O. sativa L. and O. glaberrima. In order to clarify the repetitive sequences in the genome distribution and structural characteristics, three kinds of repeats C₀t-1 DNA, rDNA and ITS were utilized to perform sequence analysis and cytogenetic positioning. This work is helpful for the establishment of a new research tool to rearch the phylogenetics of Oryza, the further study of genome and genetic relationship between rice varieties, promoting the understanding of the genetic background, and making full use of wild rice resources and molecular genetics indicators for rice hybrid breeding. The main results are as follows:1. FISH analysis of C₀t-1 DNAThe rice C₀t-1 DNA and genomic DNA were used as probes to make comparative analyses of O. punctata and O. brachyantha genome. On one hand, homologous category on karyotype analysis of O. sativa, O. punctata and O. brachyantha was carried out based on the C₀t-1 DNA hybridizational signal bands, the results show that C₀t-1 DNA most distributed on centromere, area near centromere and telomere. On the other hand, comparative analyses according to C₀t-1 DNA and genomic DNA signals indicated the relationship between genome A and genome B is much closer than that of between genome A and genome F. The feasibility of the investigation of relationships between species in the genus was confirmed by using highly and moderately repetitive DNA sequences, C₀t-1 DNA.2. FISH analysis of C₀t-1 DNAFISH was applied to somatic chromosomes preparations of O. sativa, O. glaberrima, O. officinalis, O. punctata, O. alta, O. latifolia and a F1 hybrid (ACC) with 5S rDNA and 45S rDNA as probes. We determined the numbers and position of 5S rDNA and 45S rDNA on the chromosomes, and the relationship of revolution of rDNA was also discussed. In addition, the results revealed that the 45S rDNA sites were more polymorphous than 5S rDNA sites. Owing to rapid concerted evolution of 5S rDNA, the repeat units have homogenized or nearly so in most species. However, the relatively slow concerted evolution of 45S rDNA, and the repeat units have heterozygosity. The polymorphism sites are helpful to the reconstruction of reticulate evolution and the detection of the speciation via hybridization and polyploidization.3. ITS sequence analysisIn order to conduct phylogenetic analyses of the diploid species in the O. officinalis complex based on ribosome ITS sequences, we amplified and sequenced the complete ITS sequence of the 5 diploid species by polymerase chain reaction (PCR) technique. Sequence results showed that the complete ITS sequences had relative high homology, while 5.8S rDNA had only several base mutations, ITS1 and TS2 had slightly more differentiation. Further more, phylogenetic relationship of these diploid species was estimated according to the dendrogram constructed from the ITS sequencing data. O. officinalis and O. alta were clustered together, showing close sequence homology. O. punctata, O. brachyantha and O. australiensis were clustered together, while ITS sequence homology between O. punctata and O. brachyantha was more closer than that between O. punctata and O. australiensis.