Comparative Genomes Analysis Of Different Wild Rice(Oryza) By SSR Technology

In this paper,five different genome (AA, BB, CC, BBCC, CCDD), a total of 25 kinds of rice species were used as research materials, including O.nippobare,9311, O.globerrima, O.rufipogon, 0.punctuta, 0.officinalia, O.mmuta,O. latifolia,O. alta and O. grandiglumis . Microsatellite molecular marker(SSR) which were developed in cultivated rice genome were applied to perform comparing SSR analysis and sequencing analysis to five different wild rice genomes, so as to explore the distribution of microsatellite molecular marker (SSR) in different genome wild rice, constructing the phyletic evolution diagram of different wild rice genomes, defineing the genetic relationship among 25 kinds of rice species,and investigating the reason of the differet genomes differentiation through DNA molecular variation. This work is also helpful for providing certain evidence for the underlying genetic events. The main results are as following:1.Polymorphism analysis and construction of evolutionary tree by SSR in different wild riceSSR were applied to perform comparing SSR analysis and sequencing analysis to five different wild rice genomes.There wre 434 alleles at the 70 loci investigated. The average number of alleles per locus (Na) was 6.2 with a range from3to 10,and the value of PIC was 0.49. The number of amplification bands were different in different chromosome,the more difference ; the greater the difference, indicating that the differentiation between the two species was farther. Phylogenetic diagram analysis:the 25 material in Oryza were clustered to two group- AA genome (the similarity coefficient 0.72) and the BCD genome (the similarity coefficient 0.746). AA genome, including three cultivated rice and 12 wild rice species, BCD genome, including CC, BB, BBCC, CCDD. Six allotetraploid(CCDD) from three different places, clustering results were very close. The result of distinction among different genomes by SSR markers proved that the method was feasible. Therefore, the effective amplification of the relatively conservative SSR markers which lies in gene can be provided the basis for studing the evolutionary relationship of the different rice genome.2. Sequencing analysis of the SSR which present in functional geneTo further explore the functional differentiation of certain genes in the different wild rice, four SSR locis which present in functional gene were selected to genome sequencing. The results showed that microsatellite sequence length is variable, micro-satellite DNA sequences of the wild rice genome and rice AA genome are rather conservative, but there are variations, which the main reason for this result are microsatellite sequence motifs number of changes, insertions and deletions , base substitution mutations. To some extent,this difference in length reflects the amount of the difference between the different genomes by comparing the SSR sequence motif size and number of repeat sequences, SSR repeat motif which can be seen in the cultivated rice and wild rice has a very Highly conservative.Precisely because of the similarity or conservation of the microsatellite flanking sequences, it makes a lot of SSR markers developed in rice genome can be applicated in the wild rice genome.3. Application of SSR markersIn the hybrid progenyof the O. sativa and 0.officinalia, we obtained a leaf plants. We constructed two gene pools, in theory, two DNA pools which wre made up by two extremes individuals were equivalent to two near-isogenic lines. Then 413 pairs of SSR primers were synthesized , polyacrylamide gel electrophoresis through the gene pool in the leaf and leaf of peace between the initial screening the markers that showed polymorphism between the the roll leaf gene pool and the flat leaf gene pool. A total of 6 polymorphism SSR marker were identified in markers selected, which were distributed in the three chromosomes, namely chromosome 1,5,11. We constructed a BC6F2 segregation population, results showed that the separation of roll leaf and flat leaf generally closed to the theoretical value of the ratio (1:1) in the progeny segregating populations, and extraction of plant populations 490 genomic DNA, using these markers to scan genomic DNA the 490 plants, determine SSR markers which are completely linked with the phenotype.