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

Abstract

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. IntroductionTobacco is an important cash crop in China as well as around the world, being cultivated in more than 100 countries. In addition, a recent study investigated the use of tobacco as a potential biofuel crop [1]. It is also recognized as an established model plant for physiological and genetic studies. Drought is one of the major abiotic stresses affecting crop growth, development, yield and quality, and in extreme cases, causes crop failure. In response to environmental extremes, plants have adapted several mechanisms allowing them to survive adverse conditions. Although much research has been dedicated to elucidating plant gene expression during exposure to dry conditions, the mechanisms underlying the regulation of gene expression largely remain unknown. DOI 10.1515/biol-2015-0035 Received November 11, 2014 accepted March 8, 2015 Abstract: 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 wellknown. 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