Comparative Transcriptional Analysis of Two Contrasting Rice Genotypes in Response to Salt Stress

Abstract

Improving rice salt-tolerance is an effective way to deal with the increasing food demand caused by soil salinization and population growth. Nevertheless, the molecular mechanisms of rice salt-tolerance remain elusive. In this study, comparative transcriptomic analyses were performed to identify salt-tolerance genes that were either specifically regulated or more changed in salt-tolerant cultivar FL478 relative to salt-sensitive cultivar 93-11. In total, 1423, 175, and 224 salt-tolerance genes were identified under 200 mM NaCl treatment for 6 h, 24 h, and 72 h, respectively. These genes were commonly enriched in transport and peroxidase/oxidoreductase activity across all timepoints, but specially enriched in transcription regulator activity at 6 h under salt stress. Further analysis revealed that 53 transporters, 38 transcription factors (TFs), and 23 reactive oxygen species (ROS) scavenging enzymes were involved in salt adaptation of FL478, and that overall, these salt-tolerance genes showed a faster transcriptional expression response in FL478 than in 93-11. Finally, a gene co-expression network was constructed to highlight the regulatory relationships of transporters, TFs, and ROS scavenging genes under salt-stress conditions. This work provides an overview of genome-wide transcriptional analysis of two contrasting rice genotypes in response to salt stress. These findings imply a crucial contribution of quickly transcriptional changes to salt tolerance and provide useful genes for genetic improvement of salt tolerance in rice.

Alternative splicing as a driver of natural variation in abscisic acid response

“…Globally, our analysis of the RNA‐seq data revealed a reduction of approximately 21% and 32% in the number of differentially expressed and differentially spliced genes, respectively, clearly showing that ABA induced fewer changes not only in gene expression but also in alternative splicing in the least ABA‐sensitive accession, Kn‐0. Transcriptomic studies comparing natural variants with opposite stress sensitivities have been essentially conducted in other plant species and with inconsistent results—genotypes more sensitive to an osmotic stressor, such as salt, do not always change their expression and splicing patterns in response to stress than tolerant cultivars (Kaundal et al., 2021; Kong et al., 2021; Li et al., 2018; Mirdar Mansuri et al., 2019; Shankar et al., 2016; Ye et al., 2022; Zhang et al., 2021). Nonetheless, these studies largely agree on the importance of the stress‐tolerant variant activating genes with relevant stress functions.…”

RVE1, DBB1b, and COL2 Transcription Factors Are Responsive to Combined Stress by UV-B Radiation and Cold in Bell Pepper (Capsicum annuum)

“…For example, Liu et al reported 17 TFs as hub genes of maize drought stress adaptation with WGCNA [28]. Moreover, one and nine candidates hub TFs related to salt response in rice have been detected using WGCNA [29,30]. Likewise, the use of WGCNA focused on the study of hub TFs has helped to improve the response of plants to abiotic stress.…”