Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress [Total RNA]

Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism. Overall design: Using RNA-Seq, we analyzed transcriptome of the total RNA as well as the RNA-associated with the polysomes (PS) from the control and salt-exposed Pokkqli and IR29 seedlings.

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Li YF, Zheng Y, Vemireddy LR, Panda SK, Jose S, Ranjan A, Panda P, Govindan G, Cui J, Wei K, Yaish MW, Naidoo GC, Sunkar R