Consummation Of Local Bioinformatic Platform And Analysis Of Large-scale Data From Rice

In the past decennary our laboratory has accumulated a great number of experimental data, constructed a normalized whole-life-cycle cDNA library by use of 15 tissues of rice cultivar Minghui 63 and established a rice mutant pool which contained over 129,000 individual lines. These provided well groundwork for setting up a local bioinformatic platform and systematic analysis of large-scale data from rice. Based on the previous work, this study mainly performed some work as follows:1. Random sequencing from 5' ends of more than 40,000 cDNA clones of the normalized cDNA library generated 39,208 expressed sequnce tags (EST) . Then Rice EST database (REDB, http://redb.ncpgr.cn ) was constructed by using these data.2. After trimming, processing and analysis by using ESTClustering program, 17,835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific.3. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank by using three methods revealed a large number of polymorphism(deletion/insertion/substitution) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was found to be higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of polymorphism was highly variable among different rice varieties by using different methods.4. In total, 15,726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.5. The indica subspecies of cultivated rice occupies the largest area of rice production in the world. This study is the first time that performing a systematic...