Discovery of Differentially Expressed Genes Under Salt Stress Conditions Employing mRNA and Polysome RNA-Seq in Rice

Soil salinity is one of the primary causes of production decline in rice, a staple crop for over half of the world’s population. Naturally adapted salt-tolerant relatives are potential sources for elucidating gene regulatory networks important for salinity tolerance. Rice has offered considerable genetic diversity with respect to salt tolerance; Pokkali is a highly salt-tolerant genotype whereas IR29, a genotype that is widely used for cultivation, is highly salt-sensitive. Because salinity tolerance is a complex trait, genome-wide transcriptome analysis can offer better understanding of the molecular basis of salt tolerance. To gain an insight into the gene expression changes that occur in response to salt stress not only at the transcriptional level but also at the translational level, we performed RNA-seq and polysome RNA-seq from seedlings of Pokkali and IR29 that are salt-treated and untreated samples.  This analysis yielded number of differentially expressed genes (DEGs) in both the genotypes. In general, the number of upregulated genes was much larger than those of down regulated genes. The largest number of DEGs was observed in Pokkali (1218) compared to IR29 (1019).  Interestingly, 764 DEGs (453 in the total RNA population and 311 in the polysomal-associated RNA populatoon) were specific to Pokkali while only 240 DEGs (173 in the total RNA population and 167 in the polysomal-associated RNA fraction) were specific to IR29. The gene onotology (GO) for the enriched pathways include ROS homeostasis, cell wall biosynthesis, photosynthesis, signal transduction, as well as ion transport and there are specific differences between Pokkali and IR29 with respect to these pathways.