Analysis of global gene expression profiles in tobacco roots under drought stress

Tobacco (Nicotiana tabacum L.) is an economically important and relatively drought-tolerant crop grown around the world. However, the molecular regulatory mechanisms involved in tobacco root development in response to drought stress are not well-known. To gain insight into the transcriptome dynamics associated with drought resistance, genome-wide gene expression profiling of roots from a tobacco cultivar (Honghua Dajinyuan, a major flue-cured tobacco cultivar in Southwest China) under 20% PEG6000 treatment for 0, 6 h and 48 h were conducted using Solexa sequencing (Illumina Inc., San Diego, CA, USA). Over five million tags were generated from tobacco roots, including 229,344, 221,248 and 242,065 clean tags in three libraries, respectively. The most differentially expressed tags, with either log2FC > 2.0 for up-regulated genes or log2FC < -2.0 for down regulated genes (p < 0.001), were analyzed further. In comparison to the control, 1476 up-regulated and 1574 down-regulated differentially expressed genes (DEGs) were identified, except for unknown transcripts, which were grouped into 43 functional categories involved in seven significant pathways. The most enriched categories were those that were populated by transcripts involved in metabolism, signal transduction and cellular transport. Many genes and/or biological pathways were found to be common among the three libraries, for example, genes participating in transport, stress response, auxin transport and signaling, etc. Next, the expression patterns of 12 genes were assessed with quantitative real-time PCR, the results of which agreed with the Solexa analysis. In conclusion, we revealed complex changes in the transcriptome during tobacco root development related to drought resistance, and provided a comprehensive set of data that is essential to understanding the molecular regulatory mechanisms involved. These data may prove valuable in future studies of the molecular mechanisms regulating root development in response to drought stress in tobacco and other plants.