National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China.
Plant J. 2010 Mar;61(5):752-66. doi: 10.1111/j.1365-313X.2009.04100.x. Epub 2009 Dec 9.
Growth and development of a plant are controlled by programmed expression of suits of genes at the appropriate time, tissue and abundance. Although genomic resources have been developed rapidly in recent years in rice, a model plant for cereal genome research, data of gene expression profiling are still insufficient to relate the developmental processes to transcriptomes, leaving a large gap between the genome sequence and phenotype. In this study, we generated genome-wide expression data by hybridizing 190 Affymetrix GeneChip Rice Genome Arrays with RNA from 39 tissues collected throughout the life cycle of the rice plant from two varieties, Zhenshan 97 and Minghui 63. Analyses of the global transcriptomes revealed many interesting features of dynamic patterns of gene expression across the tissues and stages. In total, 38 793 probe sets were detected as expressed and 69% of the expressed transcripts showed significantly variable expression levels among tissues/organs. We found that similarity of transcriptomes among organs corresponded well to their developmental relatedness. About 5.2% of the expressed transcripts showed tissue-specific expression in one or both varieties and 22.7% of the transcripts exhibited constitutive expression including 19 genes with high and stable expression in all the tissues. This dataset provided a versatile resource for plant genomic research, which can be used for associating the transcriptomes to the developmental processes, understanding the regulatory network of these processes, tracing the expression profile of individual genes and identifying reference genes for quantitative expression analyses.
植物的生长和发育受特定时间、组织和丰度下基因表达程序的控制。尽管近年来在模式作物水稻的基因组研究中迅速开发了基因组资源，但基因表达谱的数据仍然不足以将发育过程与转录组联系起来，导致基因组序列与表型之间存在很大差距。在这项研究中，我们通过将来自两个品种（珍汕 97 和明恢 63）的整个生命周期中收集的 39 种组织的 RNA 与 190 个 Affymetrix GeneChip Rice Genome Arrays 杂交，生成了全基因组表达数据。对全球转录组的分析揭示了组织和阶段之间基因表达动态模式的许多有趣特征。总共检测到 38793 个探针集作为表达，并发现 69%的表达转录本在组织/器官之间表现出显著的可变表达水平。我们发现器官之间的转录组相似性与其发育相关性很好。约 5.2%的表达转录本在一个或两个品种中表现出组织特异性表达，22.7%的转录本表现出组成型表达，包括 19 个在所有组织中高且稳定表达的基因。该数据集为植物基因组研究提供了一个通用的资源，可以用于将转录组与发育过程相关联，理解这些过程的调控网络，追踪单个基因的表达谱，并识别定量表达分析的参考基因。
