Deep Transcriptional Profiling of Rice Using Signature Sequencing

作为一种养活全球一半以上人口的农作物，以及在美国作为具有重要经济意义的谷类作物的典范，水稻非常重要。最近基因组序列的可用性促进了水稻基因的功能分析和分子研究。然而，这些基因中的大多数还只是通过计算而不是实验方法来定义的；计算基因预测可能无法识别染色体序列内的所有RNA转录本。该项目将使用一种称为“大规模平行特征测序”（MPSS）的转录分析技术来表征水稻转录本的多样性和表达模式。确定水稻基因组中基因表达的模式和水平将促进我们对水稻分子生物学和控制重要农艺性状的遗传因子的理解。这种对水稻的分析对其他经济上重要的谷物，如玉米、小麦、高粱和大麦的改良具有广泛的实际意义，因为在这些物种中存在的几乎所有基因都可能在水稻中有同源物。MPSS数据将用于识别计算方法遗漏的基因，并将提供验证先前预测但从未在实验中证实的许多基因的数据。MPSS将用于评估在以下条件下的基因表达：在不同的未经处理的水稻组织和这些组织的一个子集在寒冷、干旱和盐胁迫下。-真菌或细菌感染的水稻组织在易感和抗性植物。将在感染或耐药性反应期间测定一系列时间点。在“籼稻”和籼稻与粳稻杂交的背景下；该实验将测量两个水稻品种之间基因表达的差异，这两个水稻品种的基因组序列是可用的。MPSS技术鉴定的新转录本将通过微阵列分析和500多个新转录本测序进行验证。所有这些数据（MPSS、微阵列和转录本序列验证）将通过项目网页公开提供。该网站将包括查询和分析工具，以方便公众使用水稻MPSS数据，并将显示水稻MPSS特征的丰度和染色体位置。这个网站将类似于我们为拟南芥模型开发的网站（http://www.dbi.udel.edu/mpss）。

Rice is important both as a crop plant that feeds more than half of the world's population and as a model for cereal crops of great economic importance in the US. The recent availability of the genomic sequence facilitates functional analysis and molecular studies of the rice genes. However, most of these genes are as yet defined only by computational and not experimental approaches; computational gene predictions may not identify all RNA transcripts within the chromosomal sequence. This project will use a transcriptional profiling technology called "massively parallel signature sequencing" (MPSS) to characterize the diversity and expression patterns of rice transcripts. Defining the patterns and levels of gene expression in the rice genome will advance our understanding of rice molecular biology and genetic factors controlling important agronomical traits. This analysis of rice has broad practical implications for the improvement of other economically important cereals, such as corn, wheat, sorghum and barley, because nearly all genes present in these species are likely to have homologs in rice. The MPSS data will be used to identify genes missed by computational approaches and will provide data that validate many genes previously predicted but never confirmed experimentally. MPSS will be used to assess gene expression under the following conditions: -In diverse untreated rice tissues and a subset of these tissues under cold, drought and salt stress.-In fungal- or bacterial-infected rice tissues in both susceptible and resistant plants. A series of timepoints will be assayed during the infection or resistance response.-In an 'Indica' rice background and in a hybrid of Indica x Japonica; this experiment will measure differences in gene expression between the two rice varieties for which genomic sequence is available.The novel transcripts identified by the MPSS technology will be validate by microarray analysis and by sequencing more than 500 novel transcripts. All of these data (MPSS, microarray, and sequence validation of transcripts) will be made publicly available through a project webpage. This web site will include query and analysis tools to facilitate public use of the rice MPSS data and will display the abundance and chromosomal locations of rice MPSS signatures. This website will be similar to that which we have developed for the model dicot, Arabidopsis (http://www.dbi.udel.edu/mpss).