The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses

TLDR

Plant tolerance to abiotic stresses is thought to be governed by complex gene networks. The study aimed to generate a comprehensive Arabidopsis transcriptome dataset to elucidate regulatory networks and provide an overview of stress‑induced gene expression patterns. Arabidopsis plants of identical genotype were exposed side‑by‑side to a kinetic series of stresses (heat, cold, drought, salt, high osmolarity, UV‑B, wounding) while tissue and RNA were harvested in parallel, and gene expression was profiled with Affymetrix ATH1 microarrays under identical protocols. The data reveal a core set of stress‑responsive genes that modulate energy balance and suggest that systemic signals from stressed tissues coordinate stress responses, making the dataset a valuable resource for plant abiotic stress research.

Abstract

Summary The tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side‐by‐side and in a high‐resolution kinetic series, Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV‐B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols. Here we describe the technical performance of the experiments. We also present a general overview of environmental abiotic stress‐induced gene expression patterns and the results of a model bioinformatics analysis of gene expression in response to UV‐B light, drought and cold stress. Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses. In addition, there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses. In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress.