Comparative analysis of salt responsive gene regulatory networks in rice and Arabidopsis.

•Based on public salt –related microArray data, small RNA-seq and degradome sequence, we constructed and compared salt-response networks in rice and Arabidopsis, consisting of miRNAs, genes and transcription factors (TFs).•In rice, more target genes of networks were enriched in development and growth, while more stress directly-related genes were detected in Arabidopsis networks.•Salt response networks of Arabidopsis are typically organized.•Salt-response mechanisms of rice are emphasized on avoiding salt stress by regulating growth and development according to rice miRNA-TF-genes networks.•MiRNA171-GRAS and miRNA169-NFYA are possible species-conserved salt-response patterns. Not only are they detected in our results, but also reported in other signaling pathways. For instance, miRNA169-NFYA is found work in ABA signaling pathways.