Comparative Transcriptome Analysis of Salt-Stress-Responsive Genes in Rice Roots

Soil salinity greatly impairs plant growth and crop productivity. Rice (Oryza sativa L.) is a salt-sensitive crop. To better understand the molecular mechanisms of salt tolerance in roots, the BGISEQ-500 sequencing platform was employed to elucidate transcriptome changes in rice roots after 0, 3, 24, and 72 h of salt stress. The results showed that root K+ content decreased and Na+ content increased rapidly after the initial stage of salt stress, but that fresh and dry weight in root did not significantly reduce. Compared to the control (no salt stress), 1,292, 453, and 486 differentially expressed genes (DEGs) were upregulated, respectively, and 939, 894, and 646 DEGs were downregulated, respectively, after 3, 24, and 72 h of salt treatment. The number of DEGs was higher during the early stage of salt stress (3 h) than in later stages (24 and 72 h). A number of DEGs involved in the response and adaptation to salt stress were related to protein kinase and calcium-binding, plant hormone signaling and metabolism, transcriptional regulation, metabolic pathways, antioxidant activity, and ion transport. Many of these DEGs were activated during the early stage of salt stress (3 h). The present study reports candidate salt-stress-responsive genes with the potential to genetically improve salt tolerance in rice elsewhere.