Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress

Abstract

Soil salinity is a major constraint to rice production worldwide; hence intensive efforts are on to identify genes that make rice varieties tolerant to the salt stress. In this study, four rice varieties differing in tolerance to salinity were studied for differential gene expression through microarray analysis of RNA extracted from rice seedlings grown under control and salt stress conditions. Overall 1,696 gene probes in the tolerant and 2,220 gene probes in the sensitive varieties showed significant differential expression under salt stress as compared to control plants, but only 72 of these were common between the tolerant and susceptible variety groups. Fifty highest responsive genes in the tolerant and sensitive variety groups included some of the well known salt responsive genes, e. g. basic proline-rich protein, zinc finger protein and late embryogenesis abundant protein. We identified 6 genes that were commonly differentially expressed under salt stress in all the four varieties studied and hence could be the nodal points for transcriptional regulation under salt stress. These included genes for FACT complex subunit SSRP1-A, ORM1, abscisic stress ripening protein, photosystem II 10 kDa protein, negative transcription regulator-like protein and purple acid phosphatase. Expression patterns of the 6 genes were similar in the four genotypes except that all of these were down regulated in the salt tolerant variety CSR 27 under salt stress, while one gene was uniquely over expressed in highly salt sensitive variety VSR 156. These lists may contain the probable candidate genes for salt tolerance.

Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees

“…One hypothetical protein (CCI6_RS13590) was up-regulated under both salt and osmotic stress conditions. In a study of differentially expressed genes in salt-tolerant and salt sensitive varieties of rice, zinc peptidase was among the 50 highest responsive genes in the salt-tolerant variety [ 74 ].…”

“…A zinc peptidase gene was among the salt-tolerant strain-specific genes that were responsive to salt stress. Transcriptome analysis of salt-tolerant and salt-sensitive varieties of rice had a zinc peptidase gene as one of the 50 top responsive genes [ 74 ]. The zinc peptidase gene up-regulated in strain CcI6 under salt stress has a DNA binding domain, suggesting it might play a role in response regulation.…”

Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

“…Some source data originated from experiments that tested different stressors ( Jain et al, 2007 ; Zheng et al, 2009 ; Dubey et al, 2010 ; Mittal et al, 2012a , b ); several time points after the exposure to the stressor ( Cho et al, 2008 ; Mustroph et al, 2010 ; Dai et al, 2012 ; Ma et al, 2012 ; Mittal et al, 2012a ); several concentrations of a stressor ( Takehisa et al, 2015 ), and/or several genotypes, usually using contrasting lines ( Pariasca-Tanaka et al, 2009 ; Frei et al, 2010a ; Cotsaftis et al, 2011 ; Pandit et al, 2011 ; Norton et al, 2014 ; Supplementary Table S1 ). In these cases, every possible contrast of stress condition versus control was treated as a separate experiment.…”

Construction of regulatory networks mediated by small RNAs responsive to abiotic stresses in rice (Oryza sativa)

“…LOC_Os01g04860 encoding a DUF647 domain containing protein was previously demonstrated to be highly responsive to salt stress (Pandit et al, 2011).…”