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Open Access Highly Accessed Research article

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

David Cohen1, Marie-Béatrice Bogeat-Triboulot1*, Emilie Tisserant2, Sandrine Balzergue3, Marie-Laure Martin-Magniette34, Gaëlle Lelandais5, Nathalie Ningre1, Jean-Pierre Renou3, Jean-Philippe Tamby3, Didier Le Thiec1 and Irène Hummel1

Author Affiliations

1 INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France

2 INRA, Nancy Université, UMR1136 Interactions Arbres Micro-Organismes, IFR 110 EFABA, F-54280 Champenoux, France

3 Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165-Université d'Evry Val d'Essonne-ERL CNRS 8196, 2 rue G. Crémieux, CP 5708, F-91057 Evry Cedex, France

4 UMR 518 AgroParisTech/INRA MIA, 16 rue Claude Bernard, F-75231 Paris Cedex 05, France

5 Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM UMR-S 665, Université Paris Diderot-Paris 7, INTS, 6 rue Alexandre Cabanel 75015 Paris, France

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BMC Genomics 2010, 11:630  doi:10.1186/1471-2164-11-630

Published: 12 November 2010

Abstract

Background

Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species.

Results

Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.

Conclusions

In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.