A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice

Abstract

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the “Drought and Salt Tolerance” TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

Piriformospora indica symbiosis improves water stress tolerance of rice through regulating stomata behavior and ROS scavenging systems

“…65 Putative target mRNAs encoded proteins involved in nutrient uptake, sodium transporters, growth regulators, auxin-responsive proteins, transcription factors involved in the import of potassium ions or the export of sodium ions into the root cells were identified. [74][75][76][77][78][79][80][81] The amounts of phytohormones, ROS scavenging enzymes, metabolites, phosphatases, kinases, ion, proton and metabolite transporters, osmolytes and lipids, as well as the genes for their biosyntheses, are targeted by beneficial fungi to promote osmotic stress tolerance responses in various symbiotic interactions including rice. 18,40,63,82,83 In summary, P. indica colonization promotes rice growth and grain production.…”

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation

“…There are 25 genes in this QTL region based on RGAP (Table S7). Among them, 15 genes have previously been shown to be either significantly differentially expressed due to salt treatment or to have different expression between cultivars (Walia et al 2007 ; Shankar et al 2016 ; Buti et al 2019 ; Campbell et al 2020 ) (Table S7). LOC_Os01g20160 ( OsHKT1; 5 ) was selected as the candidate gene as the transcript levels of this gene in 91 rice accessions are highly divergent, and RNA expression of M103 (salt sensitive cultivar) and Agami (salt tolerance cultivar) were significantly ( p < 0.001) different under both control and salt stress conditions during the panicle initiation stage (Table S7).…”

“…There were 21 genes in this QTL region. Among them, 12 genes have previously been shown to be either significantly differentially expressed due to salt treatment or to have different expression between cultivars (Walia et al 2007 ; Shankar et al 2016 ; Buti et al 2019 ; Campbell et al 2020 ) (Table S8). LOC_Os11g42790 ( OsNHX2 ) which is annotated as a monovalent cation: proton antiporter was selected as the candidate gene in this region (Fig.…”

“…LD heatmaps surrounding the peaks of these QTLs were constructed using the R package “LDheatmap” using squared Pearson's correlation coefficient ( r 2 ). The gene expression profiles of all genes within the Local LD region were obtained from different studies (Walia et al 2007 ; Shankar et al 2016 ; Buti et al 2019 ; Campbell et al 2020 ) to confirm the validity of candidate genes. The SNPs which were significantly ( p < 0.01) associated with the Na + concentration and/or Na + /K + ratio were extracted using PLINK.…”

Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

“…Numerous potential salt-responsive genes are located within qST1.1, which contains 198 ORFs, including 34 retrotransposon proteins, 26 transposon proteins, 57 expressed proteins, 9 hypothetical proteins, 7 peroxidase precursors, 5 transcription factors (TFs), namely OsMADS89 (LOC_Os01g18440), OsWRKY9 (LOC_Os01g18584), OsSPL12 (LOC_Os01g18850), OsMYB78L (LOC_Os01g19330), and OsMYBL (LOC_Os01g19970), and other genes such as PIF1 family genes, and protein kinase genes. Transcription factors play an essential role in rice development and responses to biotic and abiotic stresses [36][37][38][39]; these five TFs have been reported to respond to salt stress in rice to varying degrees [40,41]. The reactive oxygen species signaling pathway mediated by peroxidase was also critical, as it evoked a cascade of responses related to stress tolerance [42][43][44].…”