Alternative splicing is a major strategy used by eukaryotes to alter the dynamics of their transcriptome, yet there are only few systematic studies on it in plants till now.In an attempt to further understand how alternative splicing shape the dynamics of plant gene regulatory networks, we rebuilt the transcriptomes of normal and salt-treated seeding and root tissues of Arabidopsis thaliana from Illumina high-throughput sequencing data.More genes and transcript isoforms exhibited changes between seedlings and roots than under normal and salt-treated growth conditions.Several groups of genes/transcript isoforms with interesting expression change patterns were also identified, among which, many are of unknown functions.We also investigated the effects of alternative splicing in changing protein sequences and stress responsive regulatory networks.These results will facilitate further functional studies of tissue specific and salinity stress responsive genes and pathways from the aspect of transcriptomic dynamic regulation .