Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage

Abstract

Rice yield is most sensitive to salinity stress imposed during the panicle initiation (PI) stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during PI. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na + concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We also studied the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at PI stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during PI stage.

Comparative physiological analysis of salinity tolerance in rice

“…In response to salinity stress, expression of the OsHKT1;5 gene was induced in the roots, but not in the shoots, of the susceptible rice cultivar Koshihikari and the tolerant cultivar Nona Bokra (Ren et al 2005). Moreover, salinity-induced expression of OsHKT1;5 was observed in the roots and shoots of the tolerant cultivars and in the roots of the susceptible cultivar (Walia et al 2007). In the case of Arabidopsis, dissection of natural variations revealed that the levels of AtHKT1;1 expression correlated negatively with leaf Na + concentrations, as accessions with lower Na + accumulation in the leaves had abundant AtHKT1;1 transcripts (Baxter et al 2010).…”

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

“…The primary challenge, particularly for crops with large genomes, resides in assembling a genome-wide picture of the role of methylation in orchestrating the molecular response to the stressor. As with the study of other stresses, works on methylation-based responses to salt stress have, therefore, largely relied on low throughput-targeted approaches, low genome coverage or anonymous markers applied to a low number of genotypes [7,[25][26][27]33,47]. However, our use here of methylation sensitive Genotyping-By-Sequencing (ms-GBS) to study salt-induced changes in DNA methylation in m CCGG contexts has allowed us to survey methylome flux across a reasonably representative portion of the genome (Figure 2).…”

Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum)

“…Similar observations were reported in rice where, a massive change in gene expression was observed in a sensitive cultivar compared with a tolerant cultivar. 72,73 The downregulation of several genes involved in photosynthetic process suggests that it may be a regulatory response to limit further damage.…”