Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress

Abstract

Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties ‘C34’ and ‘Nona Bokra’. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety ‘IR29’. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

“…A great number of genes encoding splicing factors, miRNAs, long noncoding RNAs (lncRNAs), and transcription factors were found to undergo AS in young panicles and florets of rice (Li et al, 2021). The same genes from different rice genotypes carried out differential AS regulations in response to salt stress stimulation (Jian et al, 2022). Interestingly, not only growth conditions but also nutrition status affect AS regulation of related genes in different plants (Zhang Y. M. et al, 2012;Li H. et al, 2016;Nishida et al, 2017;Wang et al, 2019).…”

The Roles of Calcineurin B-like Proteins in Plants under Salt Stress

“…Plants undergo alternative splicing and post-translational modifications of proteins to adapt to salt stress [37,38]. These modifications modulate protein functionality, stability, and subcellular localization, enabling plants to fine-tune their response to salt-induced changes.…”

RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root

“…Previous studies have demonstrated that high salinity stress can promote the occurrence of alternative splicing of stress-responsive genes and affect the expression of the genes coding spliceosome components in Arabidopsis (Ding et al, 2014b;Feng et al, 2015;Gu et al, 2018), rice (Yu et al, 2021;Jian et al, 2022), wheat (Liu et al, 2018), Barley (Fu et al, 2019), Date Palm (Xu et al, 2021), grapevine (Jin et al, 2021), cotton (Zhu et al, 2018), Opisthopappus (Han et al, 2024), etc. However, the alternative splicing events in tomato root under salt stress remains to be resolved.…”

“…As AS can generate multiple transcripts from a single RNA precursor via exon skipping, intron retention, and selection of alternative donor site or acceptor site as well as other intricate forms of splicing ( Keren et al., 2010 ), AS eventually cause differential expression of the corresponding gene and modulate gene function via altering a protein domain or affecting the stability of the spliced transcript and the corresponding protein. Previous studies have demonstrated that high salinity stress can promote the occurrence of alternative splicing of stress-responsive genes and affect the expression of the genes coding spliceosome components in Arabidopsis ( Ding et al., 2014b ; Feng et al., 2015 ; Gu et al., 2018 ), rice ( Yu et al., 2021 ; Jian et al., 2022 ), wheat ( Liu et al., 2018 ), Barley ( Fu et al., 2019 ), Date Palm ( Xu et al., 2021 ), grapevine ( Jin et al., 2021 ), cotton ( Zhu et al., 2018 ), Opisthopappus ( Han et al., 2024 ), etc. However, the alternative splicing events in tomato root under salt stress remains to be resolved.…”