Comparative transcriptome analysis of gene responses of salt-tolerant and salt-sensitive rice cultivars to salt stress.

Salt stress is one unfavorable factor of global climate change that adversely affects rice plant growth and yield. To identify novel salt-tolerant genes and new varieties of salt-tolerant rice, a better understanding of the molecular regulation mechanism of salt tolerance in rice is needed. In this study we used transcriptome analyses to examine changes in gene expression of salt-tolerant and salt-sensitive rice plants. The salt-tolerant cultivar HH11 and salt-sensitive cultivar IR29 were treated with 200 mM NaCl solution for 0 h, 6 h, 24 h and 48 h at the three leaf stage. Physiological parameters and transcriptome were measured and analyzed after each treatment. Activity of SOD and POD, as well as the MDA and protein content of the two rice cultivars generally increased with increasing time of exposure to NaCl. Meanwhile, the APX activity first increased, then decreased in both cultivars, with maximum values seen at 6 h for IR29 and at 24 h for HH11. The GR and GPX activity of HH11 were stronger than that of IR29 in response to salt stress. The H2O2 content first increased at 0-6 h, then decreased at 6-24 h, and then increased again at 24-48 h under salt stress. Compared with IR29, SOD, POD and APX activity of HH11 was more sluggish in response to salt stress, reaching the maximum at 24 h or 48 h. The MDA, H2O2 and proline content of HH11 was lower than that of IR29 under salt stress. Relative to untreated HH11 plants (0 h) and those exposed to salt for 6 h, 24 h, and 48 h (H0-H6, H0-H24 and H0-H48), 7462, 6363 and 6636, differentially expressed genes (DEGs), respectively, were identified. For IR29, the respective total DEGs were 7566, 6075 and 6136. GO and KEGG enrichment analysis showed that metabolic pathways related to antioxidative responses and osmotic balance played vital roles in salt stress tolerance. Sucrose and starch metabolism, in addition to flavonoid biosynthesis and glutathione metabolism, showed positive responses to salt stress. Expression of two SPS genes (LOC_Os01g69030 and LOC_Os08g20660) and two GST genes (LOC_Os06g12290 and LOC_Os10g38740) was up-regulated in both HH11 and IR29, whereas expression of LOC_Os09g12660, a glucose-1-phosphate adenylyltransferase gene, and two SS genes (LOC_Os04g17650 and LOC_Os04g24430) was up-regulated differential expression in HH11. The results showed that HH11 had more favorable adjustment in antioxidant and osmotic activity than IR29 upon exposure to salt stress, and highlighted candidate genes that could play roles in the function and regulation mechanism of salt tolerance in rice.

Combined transcriptome and metabolome reveal glutathione metabolism plays a critical role in resistance to salinity in rice landraces HD961.

Rice (Oryza sativa) is one of the most important food crops around the world, which is sensitive to salt stress, especially in the seedling and booting stage. HD961 is a salt-tolerant rice landrace that grows along coastal beaches and has disease and insect pest resistance, salt tolerance, and vigorous growth characteristics. We performed a combined transcriptome and metabolome analysis to clarify salinity resistance mechanisms in cultivar HD961, which has adapted to salinity soil at the early seedling stage. The results showed that the growth and antioxidant capacity of HD961 were stronger than 9311 under salt stress (SS). Transcriptomic analysis showed that a total of 6,145, 3,309, 1,819, and 1,296 differentially expressed genes (DEGs) were identified in the groups of TH60 (control group vs. 60 mM group of HD961 for transcriptome), TH120 (control group vs. 120 mM group of HD961 for transcriptome), T60 (control group vs. 60 mM group of 9311 for transcriptome), and T120 (control group vs. 120 mM group of 9311 for transcriptome), respectively. Starch and sucrose metabolism and phenylpropanoid biosynthesis were shared in the four treatment groups based on a KEGG enrichment analysis of DEGs. In addition, alpha-linolenic acid metabolism, plant hormone signal transduction, plant-pathogen interaction, and fatty acid elongation were specific and significantly different in HD961. A total of 92, 158, 151, and 179 significantly regulated metabolites (SRMs) responded to SS in MH60 (control group vs. 60 mM group of HD961 for metabolome), MH120 (control group vs. 120 mM group of HD961 for metabolome), M60 (control group vs. 60 mM group of 9311 for metabolome), and M120 (control group vs. 120 mM group of 9311 for metabolome), respectively. The KEGG analysis showed that eight common metabolic pathways were identified in the four treatment groups, of which biosynthesis of amino acids was the most significant. Three specific metabolic pathways were identified in the HD961, including glutathione metabolism, ascorbate and aldarate metabolism, and pantothenate and CoA biosynthesis. Integrative analysis between the transcriptome and metabolome showed that glutathione metabolism was specific and significantly affected under SS in HD961. A total of seven SRMs and 48 DEGs and four SRMs and 15 DEGs were identified in the glutathione metabolism pathway in HD961 and 9311, respectively. The Pearson correlation analysis showed a significant correlation between reduced glutathione and 16 genes (12 upregulated and four downregulated genes), suggesting these genes could be candidates as salt-tolerance regulation genes. Collectively, our data show that glutathione metabolism plays a critical role in response to SS in rice. Moreover, the stronger regulative ability of related common genes and metabolites might contribute to salt resistance in HD961.