Analysis of miRNA-seq combined with gene expression profile reveals the complexity of salinity stress response in Oryza sativa

High salinity is a major abiotic stressor that affects crop productivity and quality. While proper seedling growth is critical for crop reproduction under high salinity stress. Nowadays, genes/miRNAs expression is used for studying salinity stress response in rice seedlings. However, analysis of miRNA combined with gene expression is rare. To this end, we used miRNA-seq and gene expression profile to ascertain 6335 genes (3276 genes up-regulated, 3059 genes down-regulated) and 126 miRNAs (47 miRNAs up-regulated, 79 miRNAs down-regulated) that respond to salinity stress in rice seedlings. We then used these 126 miRNAs (including the novel miRNA osa-Chr12_1506) to identify 121 differentially expressed predicted target genes. In addition, we identified 34 miRNA-target RNA pairs, consisting of 9 differentially expressed miRNAs with complementary expression patterns. Combined with previous studies, we proposed a simple model for the molecular mechanism of a 12-h salinity stress response in rice seedlings. The findings lead to a deeper understanding of the function of miRNAs and genes that respond to salinity, and contributed to the elucidation of the complex mechanisms activated by salinity stress.