- Temporal salt stress-induced transcriptome alterations and regulatory mechanisms. - We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. - Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single- molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG).. - Prolonged salt stress duration induces high number of DEGs.. - response to salt stress. - Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. - Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton.. - Conclusion: Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.. - Plant salt stress response mechanism is mainly stimulated by osmotic stress and Na + [3]. - Plants employ various mechanisms to deal with salt stress. - Salt stress also induces burst of oxidative stress by increasing production of reactive oxygen species (ROS). - Expression levels of genes related to many bio- logical processes and pathways are significantly affected by salt stress [22, 23]. - regulatory pathways to salt stress tolerance in cotton based on mRNA and miRNA networks in two contrasting cotton genotypes [16]. - Here, we investigated an upland cotton genotype under temporal salt stress. - The results provided good insights into the regulatory pathways involved in response to salt stress in cotton.. - Biochemical response to salt stress in cotton. - In this study, SOD, CAT, and POD were measured on young leaves collected at each time point under salt stress. - However, SOD activity was signifi- cantly higher under salt stress conditions (3 h, 12 h, 24 h and 48 h) when compared to the control condition (0 h) (P <. - Here, we found that the level of MDA increased until 12 h under salt stress, indi- cating that the plants experienced salt stress damage.. - Overview of the alternative splicing events and effect of salt stress treatments. - 1 Biochemical and enzymatic activity under salt stress in cotton for (A) superoxide dismutase (SOD), (B) catalase (CAT), (C) malondialdehyde (MDA) and (D) peroxidase (POD). - This result highlights the importance of AS in cotton transcriptome particularly under salt stress treat- ment. - We further investigated the effect of salt stress treat- ments on AS profiles in cotton FL transcriptome. - The number of AS events steadily increased from 0 h to 12 h under salt stress then, subsequently dropped until 48 h (Fig. - This pattern is similar to the observed antioxi- dant enzyme activities under salt stress (Fig. - c Variation of the number of AS event over a temporal salt stress time treatment. - and 48 h represent the different time points of salt stress (400 mM) duration. - Results showed that the numbers of DEGs increased with prolonging salt stress duration (Table 2). - Response to salt stress 8 11 9 7. - 4 Hormones and ROS-related pathways under salt stress. - In the JA biosynthesis pathway, 26 genes showed differential expression under salt stress. - Most of these genes were down-regulated under salt stress. - Salt stress leads to oxidation stress through over- accumulation of ROS. - Four of these genes were up-regulated in salt stress conditions (Table S7, Fig. - One catalase gene (GH_A07G1879) was up- regulated under salt stress conditions. - 5), with two up-regulated under salt stress conditions. - Fi- nally, we found two genes related to GR, both down- regulated under salt stress conditions. - Ion balance is greatly damaged after exposure to salt stress [35–44]. - threonine-protein kinase 1 (CIPK) genes showing signifi- cant differential expression under salt stress conditions (Table S8, Fig. - Three DEGs en- coding potassium transporter (HAK) were detected under salt stress (Table S8, Fig. - We found 14 NHX DEGs with various patterns of regulation under salt stress (Table S8, Fig. - Transcription factors related to salt stress. - Understanding the molecular mechanisms regulating cell wall integrity and modification could be useful for improving salt stress tolerance in plants. - We found 235 DEGs related to cell wall biosyn- thesis and modification under salt stress (Table S8). - We found seven DEGs related to lignin catab- olism under salt stress (Table S10). - We found 21 expansin genes showing differential expression under salt stress.. - We found 42 DEGs related to pectin catabolic process under salt stress. - We found 28 DEGs related to galacturonosyltransferase activity under salt stress (Table S10). - We found seven DEGs related to peroxidase activity under salt stress. - Receptor-like kinases have also been proved to play im- portant role in cell wall modification under salt stress [53].. - We found seven receptor-like kinase genes showing signifi- cant differential expression under salt stress (Table S10).. - Nine out of ten genes related to cell wall structural proteins were up-regulated under salt stress. - These signal molecules activate salt stress tolerance mechanism related genes. - A signifi- cant number of DEGs were found under salt stress at each time point. - Increased level of ABA in plant under salt stress promotes membrane stability and Ca + uptake [34]. - Regulation of ABA biosynthesis genes under salt stress depicts their crucial role in stress tolerance mechanism.. - Salt stress increases Na + concentration in the cytosol.. - Salt stress changes the free Ca + concentration in the cytosol. - Potassium transporters and channels (AKT, HAK, KAT) and SOS pathway related genes (CIPK, CML) showed significant differential ex- pression under salt stress. - Regulation of these genes under salt stress is consistent with previous studies . - Salt stress also induces bursts of oxidative stress by in- creasing the production of ROS [70]. - These results are consistent with previous study in which over- expression of GhSOD1 and GhCAT1 increases salt stress tolerance in cotton plants [71]. - Together with other signaling pathways, ROS scavenging mechanism confers salt stress tolerance [75].. - Transcription factors (TF) are very important elements for salt stress tolerance. - WRKY transcription factors have been reported to play an important role in salt stress tolerance mechanism [76, 77]. - Our study reports 24 TF families showing differential expression under salt stress. - Three members of bHLH family were up-regulated under salt stress. - Various members of bHLH family (VvbHLH1, CgbHLH001, EcbHLH57, and TbHLH39) enhance salt stress tolerance in transgenic plants [78–81]. - Understanding the regula- tory mechanisms responsible for cell wall remodelling under salt stress can be valuable for the improvement of salt stress tolerance mechanisms. - Our study revealed some key genes related to cell wall remodelling, differen- tially expressed under salt stress. - Most of the genes related to cellulose biosynthesis and catabolic process were down-regulated under salt stress. - A significant number of expansins and xyloglucan genes were up- regulated under salt stress. - [82], we have proposed a hypothetical salt stress tol- erance network in cotton (Fig. - Salt stress stimulus is re- ceived by sensors in plasma membrane. - ROS production is stimulated with the induction of salt stress. - Salt stress also activates Ca 2+ signaling. - Our study reports a wealth of novel transcripts and some key genes showing differen- tial expression under salt stress. - Hormone biosynthesis pathways were observed to play active role under salt stress. - We also found sodium/proton antiporter genes, potassium and calcium channels, and SOS pathway re- lated genes showing differential expression under salt stress. - DEGs related to hormone biosynthesis (ABA, NCED, PSY, AOC, SPD1), ion homeostasis (CIPK, CML, HAK, AKT, NHX), antioxidant activity (POD, SOD, CAT, GR), transcription factors (MYB, WRKY, AP2) and cell wall modification were implicated in response to salt stress. - Salt concentration of 400 mM was finally selected to induce salt stress. - 6 Hypothetical salt stress tolerance mechanism in cotton. - Differentially expressed transcription factors under salt stress.. - Differentially expressed genes related to cell wall modification under salt stress.. - Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology. - Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves. - Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. - RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii, vol. - Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L. - De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. - Comparative transcriptome analyses of barley and rice under salt stress. - Gene expression profiles during the initial phase of salt stress in rice. - Unraveling salt stress signaling in plants. - A mechanism for sustained cellulose synthesis during salt stress.. - The FERONIA receptor kinase maintains cell-wall integrity during salt stress through Ca2+ signaling. - Progress and perspective on drought and salt stress tolerance in cotton. - The potassium transporter OsHAK21 functions in the maintenance of ion homeostasis and tolerance to salt stress in rice. - Elucidating the molecular mechanisms mediating plant salt- stress responses. - Salt stress responsiveness of a wild cotton species (Gossypium klotzschianum) based on transcriptomic analysis. - Global analysis of WRKY genes and their response to dehydration and salt stress in soybean
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