Study On Hybrid Rice Finger Printing Maps & New Molecular Markers In Rice(Oryza Sativa L.)

189 pairs of Micro-satellite Primers(SSR) were used to screen the polymorphism between 93-11 and Pei' ai64S,which were the parents of Liang You Pei Jiu. There were 25 pairs of SSR primers,which showed polymorphism between the two varieties. So,the polymorphism rate was 13%. According to necessary,the polymorphisms among 13 widely used hybrid rices were analyzed by 6 pairs of primers and their finger printing maps were constructed. Generally,13 varieties can be identified by the 6,SSR primers.The new polymorphism markers (SNPs & InDels) were searched separately between the chloroplast and nuclear genome sequences using the self-compiled software (SNP_CROSS. PL). The varieties used to mine new polymorphism markers were 93-11,Guanglu' ai,Pei' ai64S and Nipponbare. Their sequences were got from BGI (Beijing Genome Institute) and NCBI(National Center of Biotechnology Information). Andwhat' s more,the partial PCR primers were designed to test polymorphism sites. The detail results were as follows:1. The comparing results among the three chloroplast genome sequence 93-11,Pei' ai64S,and Nipponbare showed that the chloroplast genome sequences were comparatively conserved:The length of the InDels were changed from 2bp-69bp;there were 57,152 201 SNPs,respectively,among 93-11 & Pei' ai64S, Pei' ai64S & Nipponbare, 93-11 & Nipponbare. These differences were analyzed.2. The polymorphism results between Guanglu' ai and Nipponbare indicated that the insertion and deletion of the repeat sequences,especially transposons,among rice genome were the main reasons which results to the difference between Indica and Japonica varieties in genomic level (about3. 1.15 million Pei' ai64S reads were compared to the Nipponbare chromosome 1(about 50.8 Mb) and 56979 SNPs were found.4. 10,000 Pel' ai64S reads were compared to the part sequence of 93-11 genome Contigs and 4196 SNPs & 2956 InDels were found. Consequently, the polymorphism conditions between the two genomes were estimated.5. Two pairs of PCR primers have validated the existence of 69 bp deletion and 32 bp insertion in 93-11 chloroplast. The PCR results among different varieties conformed that the polymorphism sites existed truly between Indica and Japonica varieties,at the same time,these results also proved that it was feasible to search polymorphism sites by sequence comparison.