【作者】 张建伟；

【导师】 王石平；

【作者基本信息】 华中农业大学 ， 生物化学与分子生物学， 2006， 博士

【摘要】 本实验室在过去的十年里积累了大量的实验数据，先后构建了一个用籼稻明恢63全生育期的15个组织制备的平衡化cDNA文库和一个含有12万多水稻突变体家系的资源库，这为建立本地化的生物信息学平台和系统分析大批量水稻数据提供了良好的基础。在前人的基础上，本研究主要从以下几个方面开展了工作： 1．随机对明恢63均一化cDNA文库超过4万个克隆进行5’末端测序，获得了39208条籼稻表达序列标签(EST)，构建了一个基于这些数据的水稻EST数据库(REDB, http://redb.ncpgr.cn)。 2．将原始EST序列，通过去污染、精处理及应用ESTClustering程序分析，得到了17835条唯一序列，每条序列都初步认为代表一个唯一基因。在这些序列中，2663条是新的，并且至少70条是籼稻所特有的。 3．用三种方法将明恢63序列与大量来自GenBank中的EST和全长cDNA比较，在亚种间和亚种内水平均发现了大量插入、缺失和替换等多态性现象。对比全部的表达序列间的多态性，亚种间的出现频率要高于亚种内的。但是，不同的分析方法以及在不同水稻品种进行各种多态性分析的结果是不稳定的。 4．总共有15726条唯一序列，包括697新的序列，被定位到前人工作中检测到的大量农艺性状的数量性状位点(QTL)所在区间。这些结果可用于开发遗传图谱上的新分子标记，检测与水稻品种间表型变异相关的等位多态性，以及通过候选基因法来加快QTL克隆。 5．籼亚种栽培稻占有世界水稻产品的最大面积，本研究首次对来自籼亚种水稻cDNA序列进行的系统分析，因此将对所有EST序列系统分析的结果包括聚类信息、功能分类、多态性数据、染色体定位信息、EST和QTL整合图谱等信息都集成到了水稻EST数据库中。 6．收集了大约12.9万个由Enhancer trap系统得到的T-DNA插入突变体信息，构建了集管理和检索为一体的水稻突变体数据库(RMD, http://rmd.ncpgr.cn)。收集到水稻突变体数据库的信息包括突变体表型、报告基因表达模式、T-DNA插入位点的侧翼序列、种子等，这些都可以在网站上通过各自的ID、关键词、核苷酸序列或蛋白质序列检索得到。更多还原

【Abstract】 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更多还原