Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Abstract Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. Conclusion The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

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Transcription Factor GarWRKY5 Is Involved in Salt Stress Response in Diploid Cotton Species (Gossypium aridum L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20215244 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5244 ◽

Cited By ~ 1

Author(s):

Qi Guo ◽

Liang Zhao ◽

Xinqi Fan ◽

Peng Xu ◽

Zhenzhen Xu ◽

...

Keyword(s):

Salicylic Acid ◽

Salt Stress ◽

Stress Response ◽

Jasmonic Acid ◽

Gene Silencing ◽

Stress Tolerance ◽

Virus Induced Gene Silencing ◽

Wild Type ◽

Salt Stress Tolerance ◽

Salt Stress Response

Cotton is one of the most economically important crops in the world, and it is exposed to various abiotic stresses during its lifecycle, especially salt stress. However, the molecular mechanisms underlying cotton tolerance to salt stress are still not fully understood due to the complex nature of salt response. Therefore, identification of salt stress tolerance-related functional genes will help us understand key components involved in stress response and provide valuable genes for improving salt stress tolerance via genetic engineering in cotton. In the present study, virus-induced gene silencing of GhWRKY5 in cotton showed enhanced salt sensitivity compared to wild-type plants under salt stress. Overexpression of GarWRKY5 in Arabidopsis positively regulated salt tolerance at the stages of seed germination and vegetative growth. Additionally, GarWRKY5-overexpressing plants exhibited higher activities of superoxide dismutase (SOD) and peroxidase (POD) under salt stress. The transcriptome sequencing analysis of transgenic Arabidopsis plants and wild-type plants revealed that there was enriched coexpression of genes involved in reactive oxygen species (ROS) scavenging (including glutamine S-transferases (GSTs) and SODs) and altered response to jasmonic acid and salicylic acid in the GarWRKY5-OE lines. GarWRKY5 is involved in salt stress response by the jasmonic acid- or salicylic acid-mediated signaling pathway based on overexpression of GarWRKY5 in Arabidopsis and virus-induced gene silencing of GarWRKY5 in cotton.

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Overexpression of the DEAD-Box RNA Helicase Gene AtRH17 Confers Tolerance to Salt Stress in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms19123777 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3777 ◽

Cited By ~ 6

Author(s):

Linh Nguyen ◽

Hye-Yeon Seok ◽

Dong-Hyuk Woo ◽

Sun-Young Lee ◽

Yong-Hwan Moon

Keyword(s):

Salt Stress ◽

Stress Response ◽

Stress Tolerance ◽

Stress Responses ◽

Rna Helicase ◽

Activation Tagging ◽

Salt Stress Tolerance ◽

Salt Stress Response ◽

Dead Box ◽

Stress Responsive Genes

Plants adapt to abiotic stresses by complex mechanisms involving various stress-responsive genes. Here, we identified a DEAD-box RNA helicase (RH) gene, AtRH17, in Arabidopsis, involved in salt-stress responses using activation tagging, a useful technique for isolating novel stress-responsive genes. AT895, an activation tagging line, was more tolerant than wild type (WT) under NaCl treatment during germination and seedling development, and AtRH17 was activated in AT895. AtRH17 possesses nine well-conserved motifs of DEAD-box RHs, consisting of motifs Q, I, Ia, Ib, and II-VI. Although at least 12 orthologs of AtRH17 have been found in various plant species, no paralog occurs in Arabidopsis. AtRH17 protein is subcellularily localized in the nucleus. AtRH17-overexpressing transgenic plants (OXs) were more tolerant to high concentrations of NaCl and LiCl compared with WT, but no differences from WT were detected among seedlings exposed to mannitol and freezing treatments. Moreover, in the mature plant stage, AtRH17 OXs were also more tolerant to NaCl than WT, but not to drought, suggesting that AtRH17 is involved specifically in the salt-stress response. Notably, transcriptions of well-known abscisic acid (ABA)-dependent and ABA-independent stress-response genes were similar or lower in AtRH17 OXs than WT under salt-stress treatments. Taken together, our findings suggest that AtRH17, a nuclear DEAD-box RH protein, is involved in salt-stress tolerance, and that its overexpression confers salt-stress tolerance via a pathway other than the well-known ABA-dependent and ABA-independent pathways.

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Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽

10.3390/molecules26040782 ◽

2021 ◽

Vol 26 (4) ◽

pp. 782

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Myung Geun Ji ◽

Gyeong-Im Shin ◽

Song Yi Jeong ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Humic Acid ◽

Stress Tolerance ◽

Plant Development ◽

Molecular Mechanisms ◽

Abiotic Stress Tolerance ◽

Principal Component ◽

Salt Stress Tolerance ◽

Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

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Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud.

10.21203/rs.2.16313/v3 ◽

2020 ◽

Author(s):

Jingjing Wang ◽

Cong An ◽

Hailin Guo ◽

Xiangyang Yang ◽

Jingbo Chen ◽

...

Keyword(s):

Signal Transduction ◽

Salt Stress ◽

Stress Response ◽

Salt Tolerance ◽

Molecular Mechanisms ◽

Salt Tolerant ◽

Zoysia Japonica ◽

Salt Stress Response ◽

Leaves And Roots ◽

Time Point

Abstract Background: Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown. Results: The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family. Conclusions: Z011 may have improved salt tolerance by reducing Na+ transport from the roots to the leaves, increasing K+ absorption in the roots and reducing K+ secretion from the leaves to maintain a significantly greater K+/Na+ ratio. Twenty-four hours might be a relatively important time point for the salt-stress response of zoysiagrass. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation. This study provides fundamental information concerning the salt-stress response of Zoysia and improves the understanding of molecular mechanisms in salt-tolerant plants.

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Meta-Analysis of Salt Stress Transcriptome Responses in Different Rice Genotypes at the Seedling Stage

Plants ◽

10.3390/plants8030064 ◽

2019 ◽

Vol 8 (3) ◽

pp. 64 ◽

Cited By ~ 8

Author(s):

Weilong Kong ◽

Hua Zhong ◽

Ziyun Gong ◽

Xinyi Fang ◽

Tong Sun ◽

...

Keyword(s):

Salt Stress ◽

Stress Tolerance ◽

Meta Analysis ◽

Calvin Cycle ◽

Seedling Stage ◽

Mitogen Activated Protein Kinase ◽

Molecular Response ◽

Salt Stress Tolerance ◽

Salt Stress Response ◽

Rice Genotypes

Rice (Oryza sativa L.) is one of the most important staple food crops worldwide, while its growth and productivity are threatened by various abiotic stresses, especially salt stress. Unraveling how rice adapts to salt stress at the transcription level is vital. It can provide valuable information on enhancing the salt stress tolerance performance of rice via genetic engineering technologies. Here, we conducted a meta-analysis of different rice genotypes at the seedling stage based on 96 public microarray datasets, aiming to identify the key salt-responsive genes and understand the molecular response mechanism of rice under salt stress. In total, 5559 genes were identified to be differentially expressed genes (DEGs) under salt stress, and 3210 DEGs were identified during the recovery process. The Gene Ontology (GO) enrichment results revealed that the salt-response mechanisms of shoots and roots were different. A close-knit signaling network, consisting of the Ca2+ signal transduction pathway, the mitogen-activated protein kinase (MAPK) cascade, multiple hormone signals, transcription factors (TFs), transcriptional regulators (TRs), protein kinases (PKs), and other crucial functional proteins, plays an essential role in rice salt stress response. In this study, many unreported salt-responsive genes were found. Besides this, MapMan results suggested that TNG67 can shift to the fermentation pathway to produce energy under salt stress and may enhance the Calvin cycle to repair a damaged photosystem during the recovery stage. Taken together, these findings provide novel insights into the salt stress molecular response and introduce numerous candidate genes for rice salt stress tolerance breeding.

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iTRAQ-based comparative proteomic analysis reveals tissue-specific and novel early-stage molecular mechanisms of salt stress response in Carex rigescens

Environmental and Experimental Botany ◽

10.1016/j.envexpbot.2017.08.010 ◽

2017 ◽

Vol 143 ◽

pp. 99-114 ◽

Cited By ~ 20

Author(s):

Mingna Li ◽

Kun Zhang ◽

Ruicai Long ◽

Yan Sun ◽

Junmei Kang ◽

...

Keyword(s):

Salt Stress ◽

Stress Response ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Early Stage ◽

Salt Stress Response ◽

Tissue Specific ◽

Comparative Proteomic Analysis

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Heterologous Expression of Transcription Factor AtWRKY57 Alleviates Salt Stress-Induced Oxidative Damage

The Open Biotechnology Journal ◽

10.2174/1874070701812010204 ◽

2018 ◽

Vol 12 (1) ◽

pp. 204-218

Author(s):

Wei Tang

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Salt Stress ◽

Heterologous Expression ◽

Stress Tolerance ◽

Molecular Mechanisms ◽

Abiotic Stress Tolerance ◽

Thiobarbituric Acid Reactive Substance ◽

Salt Stress Tolerance ◽

Wrky Transcription Factors

Background:WRKY transcription factors play important roles in the responses to abiotic stresses, seed dormancy, seed germination, developmental processes, secondary metabolism, and senescence in plants. However, molecular mechanisms of WRKY transcription factors-related abiotic stress tolerance have not been fully understood.Methods:In this investigation, transcription factor AtWRKY57 was introduced into cell lines of rice (Oryza sativaL.), tobacco (Nicotiana tabacum), and white pine (Pinus strobesL.) for characterization of its function in salt stress tolerance. The purpose of this investigation is to examine the function of AtWRKY in a broad sample of plant species including monocotyledons, dicotyledons, and gymnosperms.Results:The experimental results demonstrated that heterologous expression of transcription factor AtWRKY57 improves salt stress tolerance by decreasing Thiobarbituric Acid Reactive Substance (TBARS), increasing Ascorbate Peroxidase (APOX) and Catalase (CAT) activity under salt stress. In rice, overexpression of transcription factor AtWRKY57 enhances expression of Ca2+-dependent protein kinase genesOsCPk6andOsCPk19to counteract salt stress.Conclusion:These results indicated that transcription factor AtWRKY57 might have practical application in genetic engineering of plant salt tolerance throughout the plant kingdom.

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Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

BMC Genomics ◽

10.1186/s12864-020-07260-z ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Delong Wang ◽

Xuke Lu ◽

Xiugui Chen ◽

Shuai Wang ◽

Junjuan Wang ◽

...

Keyword(s):

Superoxide Dismutase ◽

Salt Stress ◽

Stress Response ◽

Salt Tolerance ◽

Gossypium Hirsutum ◽

Stress Tolerance ◽

Economic Losses ◽

Salt Tolerant ◽

Salt Stress Tolerance ◽

Long Reads

Abstract Background Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. 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). Results Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. 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.

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