Dissecting the developmental transcriptomes of rice. Oryza sativa Indica Group

Transcriptional programs are important for the development of complex eukaryotic organisms. Suites of genes expressed with temporal and spatial controls by regulatory networks in response to environmental cues are the cornerstone for achieving the specification of morphology and physiology of the tissue or organ systems. Thus, an important issue of developmental biology is to define the subsets of expressed genes and their expression patterns that are related to the organ or tissue system. Rice is a model plant for cereal genome research. Although large amounts of data of whole genome expression have been generated in recent years in rice, the majority of the studies were designed to identify differentially expressed genes between controls and treatments with certain experimental conditions such as biotic, abiotic or light, or to investigate the comparative expression patterns between wild type and mutants of certain genes. Only in a few cases were the datasets designed for studying the transcriptomes of a limited number of organs and cell types. Thus, there is still insufficiency in the available datasets that would allow for the establishment of expression patterns for suits of genes during the developmental processes of rice. In this study, we collected 39 tissues/organs covering the life cycle of the rice from two indica varieties Minghui 63 and Zhenshan 97, and the Affymetrix GeneChip Rice Genome Array was used to investigate the transcriptomes of these organs. The objective was to develop a genomic resource of genome-wide dynamic transcriptome of the rice plant, which could be used as the reference gene expression map for rice and other cereals. Also, the dataset is used to identify the candidates of genes with potential functions in regulating the development of rice or breeding practice. Keywords: rice, expression profiling, life cycle, development, inflorescence Overall design: To dissect the developmental transcriptomes of rice, a total of 39 tissues covering the entire tissue culture process and life cycle were sampled from two indica varieties Minghui 63 and Zhenshan 97. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcriptomes. Two independent biological replicates were sampled from most tissues, except two seedling and three panicle tissues, for which three independent biological replicates each with two technical replicates were sampled, resulting in a dataset of 190 microarrays.

转录程序（transcriptional programs）对于复杂真核生物的发育至关重要。由调控网络进行时空调控、响应环境信号的基因集合，是实现组织或器官系统形态与生理特化的核心基础。因此，发育生物学的一项重要课题，便是明确与特定器官或组织系统相关的表达基因子集及其表达模式。

水稻是谷类作物基因组研究的模式植物。近年来，尽管已产生了大量水稻全基因组表达数据，但绝大多数研究旨在鉴定特定实验条件（如生物胁迫、非生物胁迫或光照）下对照组与处理组间的差异表达基因，或是探究野生型与特定基因突变体间的比较表达模式。仅有极少数数据集被设计用于研究有限数量的器官和细胞类型的转录组（transcriptome）。因此，当前可用数据集仍不足以支持构建水稻发育过程中各基因集的表达模式。

本研究收集了来自两个籼稻品种明恢63（Minghui 63）和珍汕97（Zhenshan 97）的、覆盖水稻全生命周期的39个组织/器官，并使用Affymetrix GeneChip水稻基因组芯片分析了这些器官的转录组。本研究的目标是构建水稻全基因组动态转录组的基因组资源，可为水稻及其他谷类作物提供参考基因表达图谱。此外，本数据集还可用于筛选在水稻发育调控或育种实践中具有潜在功能的候选基因。

关键词：水稻，表达谱，生命周期，发育，花序

整体实验设计：为解析水稻的发育转录组，本研究从两个籼稻品种明恢63和珍汕97中采集了覆盖全组织培养流程及生命周期的39个组织样本。采用Affymetrix GeneChip水稻基因组芯片分析这些样本的动态转录组。除2个幼苗组织和3个穗组织外，绝大多数组织均设置2次独立生物学重复；针对上述2个幼苗及3个穗组织，各设置3次独立生物学重复，且每个重复包含2次技术重复，最终得到包含190张微阵列芯片的数据集。