Abstract
BackgroundSoil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently.ResultsWe sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar ‘Nipponbare’ (NB) and the salt-tolerant cultivar ‘Sea Rice 86’ (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5′ ends to the 3′ ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86.ConclusionsThis study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.
Highlights
Soil salinization represents a serious threat to global rice production
Library construction with ribosome-protected mRNA fragment (RPF) from NB and Sea Rice 86’ (SR86) To determine the rice translational landscape, we performed ribo-seq and polyA RNA-seq with seedling shoots of NB and SR86 before and after 24-h salt treatment (Fig. 1a), with three biological repeats for each treatment (Additional file 1: Table S1)
Among these novel transcripts in SR86, no completely novel genes were identified. These results indicate that SR86 shares similar transcriptomic components with NB and their differences in salt tolerance are mainly attributed to differences in gene expression, which might be controlled at the transcriptional, post-transcriptional, translational or post-translational level
Summary
Soil salinization represents a serious threat to global rice production. Significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently. Crop yield is being greatly limited by soil salinization, and there is an urgent need to improve agricultural production to meet the continuously increasing global population [2]. Yang et al BMC Genomics (2021) 22:612 a better mechanistic understanding of adaptive responses to salt stress is necessary for improving crop salt tolerance
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