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

BackgroundComparative 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.ResultsUsing 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.ConclusionsIn 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.

Effect of polyploidization on morphology in two apple (Malus × domestica) genotypes

“…These observations are in accordance with studies on polyploidy in other plants: e.g. apple (Lespinasse, Noiton 1986;Blanke et al 1994), Populus (Cohen et al 2010), Citrus spp. (Allario et al 2011) and Arabidopsis (Del Pozo, RamirezParra 2014).…”

Quantitative RT-PCR analysis of 20 transcription factor genes of MADS, ARF, HAP2, MBF and HB families in moisture stressed shoot and root tissues of sorghum

“…Role of ATHB12 and ATHB7 is well-known in Arabidopsis under water stress conditions (Olsson et al 2004). Cohen et al (2010) also reported up-regulation of putative TF close to ATHB7 and ATHB12 in populous. Recently, Ariel et al (2010) recorded role of one of the HB family member HB1 in lateral root emergence in Medicago.…”

“…On the other hand, it showed downregulation in mild and severe moisture stressed shoot tissues. Cohen et al (2010) also reported up-regulation of putative NF-YA and NF-YB in drought induced populos roots and they also carried out meta analysis of genome wide expression profiling in mature leaves and root apices. Further, the TF gene PTSb00128.1 revealed homology with OsHAP2B and AtNF-YA subunit 7.…”

Comparative Transcriptome Analysis of Two Olive Cultivars in Response to Nacl Stress

“…Such a strategy mainly relies on comparative transcriptome analysis [20] using microarrays. A plethora of comparisons between salt-sensitive and salt-tolerant cultivars of model and non-model plant species such as Arabidopsis [21][22][23], rice [24], tomato [25], poplar [26], potato [27] and sugarcane [28] have been reported up to now. These reports resulted in the identification of more than 30 families of transcription factors comprising DREB, CBF, MYB, bZIP and zing-finger families which are involved in abiotic stress including salinity [29,30].…”