The conserved salt-responsive genes in the roots of Populus × canescens and Arabidopsis thaliana

• About 860 differentially expressed genes were found in salt-stressed poplar roots.
• Arabidopsis roots displayed 2010 differentially expressed genes upon salt stress.
• The common salt-responsive genes of 128 were found in the roots of both species.
• Among the common genes 98 formed a salt-responsive co-expression network.
• cis-Elements in the conserved motifs of hub genes play a role in gene co-expression.

To dissect the salt responsive genes in the roots of Populus × canescens after salt exposure and to characterize the conserved transcripts with differential expression in the roots of P. × canescens and Arabidopsis thaliana under salinity, P. × canescens grown in sandy soil was exposed to 150 mM NaCl for 18 days and the transcriptional profiling was analyzed in the roots by using a whole genome poplar array chip. The raw data of the Affymetrix Arabidopsis genome arrays were obtained from the online array data bank and statistically analysed as that of the poplar. In the roots of P. × canescens exposed to salinity, about 860 genes displayed significantly differential expression, including 647 up-regulated and 213 down-expressed genes. In the roots of A. thaliana, 1292 genes were up- and 718 down-expressed. Among the differentially expressed genes between P. × canescens and A. thaliana, a set of common genes (128 genes) showed the same change pattern in response to salinity, including 114 induced and 14 repressed genes. A salt-responsive co-expression network was constructed with 98 common genes. Among the co-expressed genes, 22 genes were defined as hub genes which were involved in fundamental biological processes such as abiotic stimulus and signal transduction. Moreover, the cis-regulatory elements were found in the conserved motifs of hub genes. These results suggest that P. × canescens and A. thaliana possess conserved salt-responsive genes and that cis-elements in the conserved motifs of hub genes play a crucial role in coordinating the co-expression of the common genes underlying the physiological acclimation to salinity in the roots of P. × canescens and A. thaliana.