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

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.

Figure 1

Ecophysiological responses. Leaf predawn water potential, leaf relative water content, leaf full turgor osmotic pressure, height growth rate, net CO₂ assimilation rate, stomatal conductance and instantaneous water use efficiency (WUE_i) were measured on a dedicated batch of trees at the harvest time point. Closed red symbols: Carpaccio, open blue symbols: Soligo; CTL, EAR, LMI, LMO: treatments. Mean ± s.e., n = 6.

Figure 2

Analysis of significant drought-driven regulation. A total of 6,725 probesets exhibited at least one significant difference in normalized signal intensity between treated and respective control arrays (t-test, Bonferroni P < 0.05). (a) Number of probesets corresponding to regulated genes in response to each condition. (b) Intensities of drought-driven regulation in each condition. Log 2 ratio distributions are shown by box-and-whisker plots. The central mark is the median, the edges are the 25th and 75th percentiles, and the whiskers extend to minimum and maximum values. Up-regulation is depicted in white and down-regulation in black.

Figure 3

Global comparison of Carpaccio and Soligo drought responses based on differential clustering analysis. DCA were performed (a) on the 3,515 probesets that were significantly regulated at least twice across the twelve conditions (t-test, Bonferroni P < 0.05); (b) on the 652 probesets that were significantly regulated in mature leaves, at least twice across the six combinations; and (c) on the 2,410 probesets that were significantly regulated in root apices at least twice across the six combinations. Complete distance matrices were combined into a single matrix (left panel with small distance in red and large distance in white). Full, partial or split conservation were given in the middle panel (blank = not conserved). Expression profiles are shown for Carpaccio and for Soligo (right panel with significant up-and down-regulation indicated in red and green, respectively).

Figure 4

Expression and regulation of drought-responsive genes in other Populus species. A. Detection of drought-regulated genes common to our study and the literature. B. Detection of organ-preferred expression through comparison of our data with the literature. C. Detection of the impact of maturity level on gene expression in interaction with organ specificity using exPlot [37]. Meta-analysis was restricted to the literature considering root and/or leaf tissues.

Figure 5

Overview of drought-regulated transcriptome responses in mature leaves and root apices of two poplar genotypes. Putative regulated processes are enclosed in boxes. For illustration, some representative genes are given in italic (The Populus genome v1.1). Gene regulation related to energy deficit response/signalling is described for arabidopsis [41,108].