Drought Stress-Mediated Transcriptome Profile Reveals NCED as a Key Player Modulating Drought Tolerance in Populus davidiana

Populus trichocarpa has been studied as a model poplar species through biomolecular approaches and was the first tree species to be genome sequenced. In this study, we employed a high throughput RNA-sequencing (RNA-seq) mediated leaf transcriptome analysis to investigate the response of four different Populus davidiana cultivars to drought stress. Following the RNA-seq, we compared the transcriptome profiles and identified two differentially expressed genes (DEGs) with contrasting expression patterns in the drought-sensitive and tolerant groups, i.e., upregulated in the drought-tolerant P. davidiana groups but downregulated in the sensitive group. Both these genes encode a 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme required for abscisic acid (ABA) biosynthesis. The high-performance liquid chromatography (HPLC) measurements showed a significantly higher ABA accumulation in the cultivars of the drought-tolerant group following dehydration. The Arabidopsis nced3 loss-of-function mutants showed a significantly higher sensitivity to drought stress, ~90% of these plants died after 9 days of drought stress treatment. The real-time PCR analysis of several key genes indicated a strict regulation of drought stress at the transcriptional level in the P. davidiana drought-tolerant cultivars. The transgenic P. davidiana NCED3 overexpressing (OE) plants were significantly more tolerant to drought stress as compared with the NCED knock-down RNA interference (RNAi) lines. Further, the NCED OE plants accumulated a significantly higher quantity of ABA and exhibited strict regulation of drought stress at the transcriptional level. Furthermore, we identified several key differences in the amino acid sequence, predicted structure, and co-factor/ligand binding activity of NCED3 between drought-tolerant and susceptible P. davidiana cultivars. Here, we presented the first evidence of the significant role of NCED genes in regulating ABA-dependent drought stress responses in the forest tree P. davidiana and uncovered the molecular basis of NCED3 evolution associated with increased drought tolerance.

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Comparative Proteomics and Physiological Analyses Reveal Important Maize Filling-Kernel Drought-Responsive Genes and Metabolic Pathways

International Journal of Molecular Sciences ◽

10.3390/ijms20153743 ◽

2019 ◽

Vol 20 (15) ◽

pp. 3743 ◽

Cited By ~ 7

Author(s):

Xuan Wang ◽

Tinashe Zenda ◽

Songtao Liu ◽

Guo Liu ◽

Hongyu Jin ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Protein Interactions ◽

Stress Responses ◽

Metabolic Pathways ◽

Storage Proteins ◽

Seed Storage Proteins ◽

Comparative Proteomics ◽

Venn Diagram ◽

Drought Tolerant

Despite recent scientific headway in deciphering maize (Zea mays L.) drought stress responses, the overall picture of key proteins and genes, pathways, and protein–protein interactions regulating maize filling-kernel drought tolerance is still fragmented. Yet, maize filling-kernel drought stress remains devastating and its study is critical for tolerance breeding. Here, through a comprehensive comparative proteomics analysis of filling-kernel proteomes of two contrasting (drought-tolerant YE8112 and drought-sensitive MO17) inbred lines, we report diverse but key molecular actors mediating drought tolerance in maize. Using isobaric tags for relative quantification approach, a total of 5175 differentially abundant proteins (DAPs) were identified from four experimental comparisons. By way of Venn diagram analysis, four critical sets of drought-responsive proteins were mined out and further analyzed by bioinformatics techniques. The YE8112-exclusive DAPs chiefly participated in pathways related to “protein processing in the endoplasmic reticulum” and “tryptophan metabolism”, whereas MO17-exclusive DAPs were involved in “starch and sucrose metabolism” and “oxidative phosphorylation” pathways. Most notably, we report that YE8112 kernels were comparatively drought tolerant to MO17 kernels attributable to their redox post translational modifications and epigenetic regulation mechanisms, elevated expression of heat shock proteins, enriched energy metabolism and secondary metabolites biosynthesis, and up-regulated expression of seed storage proteins. Further, comparative physiological analysis and quantitative real time polymerase chain reaction results substantiated the proteomics findings. Our study presents an elaborate understanding of drought-responsive proteins and metabolic pathways mediating maize filling-kernel drought tolerance, and provides important candidate genes for subsequent functional validation.

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Drought Tolerance in Wheat

The Scientific World JOURNAL ◽

10.1155/2013/610721 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 105

Author(s):

Arash Nezhadahmadi ◽

Zakaria Hossain Prodhan ◽

Golam Faruq

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Review Paper ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Glutathione S Transferase ◽

Molecular Responses ◽

Drought Tolerant ◽

Late Embryogenesis ◽

Different Types

Drought is one of the most important phenomena which limit crops’ production and yield. Crops demonstrate various morphological, physiological, biochemical, and molecular responses to tackle drought stress. Plants’ vegetative and reproductive stages are intensively influenced by drought stress. Drought tolerance is a complicated trait which is controlled by polygenes and their expressions are influenced by various environmental elements. This means that breeding for this trait is so difficult and new molecular methods such as molecular markers, quantitative trait loci (QTL) mapping strategies, and expression patterns of genes should be applied to produce drought tolerant genotypes. In wheat, there are several genes which are responsible for drought stress tolerance and produce different types of enzymes and proteins for instance, late embryogenesis abundant (lea), responsive to abscisic acid (Rab), rubisco, helicase, proline, glutathione-S-transferase (GST), and carbohydrates during drought stress. This review paper has concentrated on the study of water limitation and its effects on morphological, physiological, biochemical, and molecular responses of wheat with the possible losses caused by drought stress.

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Physiological and Proteomic Analysis Revealed the Response Mechanisms of two Different Grought-resistant Maize Varieties

10.21203/rs.3.rs-630007/v1 ◽

2021 ◽

Author(s):

Hongjie Li ◽

Mei Yang ◽

Chengfeng Zhao ◽

Yifan Wang ◽

Renhe Zhang

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Responses ◽

Molecular Chaperones ◽

Electron Flow ◽

Photochemical Efficiency ◽

Growth And Yield ◽

Protective Mechanism ◽

Drought Tolerant ◽

Maize Varieties

Abstract Background: Drought stress seriously limits the seedling growth and yield of maize. Despite previous studies on drought resistance mechanisms by which maize cope with water deficient, the link between physiological and molecular variations are largely unknown. To reveal the complex regulatory mechanisms, comparative physiology and proteomic analyses were conducted to investigate the stress responses of two maize cultivars with contrasting tolerance to drought stress. Results: Physiological results showed that SD609 (drought-tolerant) maintains higher photochemical efficiency by enhancing CEF (cyclic electron flow) protective mechanism and antioxidative enzymes activities. Proteomics analysis revealed a total of 198 and 102 proteins were differentially expressed in SD609 and SD902, respectively. Further enrichment analysis indicated that drought-tolerant ‘SD609’ increased the expression of proteins related to photosynthesis, antioxidants/detoxifying enzymes, molecular chaperones and metabolic enzymes. The up-regulation proteins related to PSII repair and photoprotection mechanisms resulted in more efficient photochemical capacity in tolerant variety under moderate drought. However, the drought-sensitive ‘SD902’ only induced molecular chaperones and sucrose synthesis pathways, and failed to protect the impaired photosystem. Further analysis indicated that proteins related to the electron transport chain, redox homeostasis and heat shock proteins (HSPs) could be important in protecting plants from drought stress. Conclusions: Our experiments explored the mechanism of drought tolerance, and obtained detailed information about the interconnection of physiological research and protein research. In summary, our findings could provide new clues into further understanding of drought tolerance mechanisms in maize.

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Physiological and Differential Proteomic Analyses of Imitation Drought Stress Response in Sorghum bicolor Root at the Seedling Stage

International Journal of Molecular Sciences ◽

10.3390/ijms21239174 ◽

2020 ◽

Vol 21 (23) ◽

pp. 9174

Author(s):

Hongbing Li ◽

Yulin Li ◽

Qingbo Ke ◽

Sang-Soo Kwak ◽

Suiqi Zhang ◽

...

Keyword(s):

Protein Synthesis ◽

Drought Stress ◽

Drought Tolerance ◽

Sorghum Bicolor ◽

Stress Responses ◽

Expression Patterns ◽

Physiological Mechanism ◽

Seedling Stage ◽

Ros Scavenging ◽

Root Response

Drought is one of the most important constraints on the growth and productivity of many crops, including sorghum. However, as a primary sensing organ, the plant root response to drought has not been well documented at the proteomic level. In the present study, we compared physiological alteration and differential accumulation of proteins in the roots of sorghum (Sorghum bicolor) inbred line BT×623 response to Polyethylene Glycol (PEG)-induced drought stress at the seedling stage. Drought stress (up to 24 h after PEG treatment) resulted in increased accumulation of reactive oxygen species (ROS) and subsequent lipid peroxidation. The proline content was increased in drought-stressed plants. The physiological mechanism of sorghum root response to drought was attributed to the elimination of harmful free radicals and to the alleviation of oxidative stress via the synergistic action of antioxidant enzymes, such as superoxide dismutase, peroxidase, and polyphenol oxidase. The high-resolution proteome map demonstrated significant variations in about 65 protein spots detected on Coomassie Brilliant Blue-stained 2-DE gels. Of these, 52 protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) representing 49 unique proteins; the levels of 43 protein spots were increased, and 22 were decreased under drought condition. The proteins identified in this study are involved in a variety of cellular functions, including carbohydrate and energy metabolism, antioxidant and defense response, protein synthesis/processing/degradation, transcriptional regulation, amino acid biosynthesis, and nitrogen metabolism, which contribute jointly to the molecular mechanism of outstanding drought tolerance in sorghum plants. Analysis of protein expression patterns and physiological analysis revealed that proteins associated with changes in energy usage; osmotic adjustment; ROS scavenging; and protein synthesis, processing, and proteolysis play important roles in maintaining root growth under drought stress. This study provides new insight for better understanding of the molecular basis of drought stress responses, aiming to improve plant drought tolerance for enhanced yield.

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Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut

BMC Plant Biology ◽

10.1186/s12870-020-02678-9 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Cuiling Yuan ◽

Chunjuan Li ◽

Xiaodong Lu ◽

Xiaobo Zhao ◽

Caixia Yan ◽

...

Keyword(s):

Transcription Factor ◽

Drought Stress ◽

Stress Responses ◽

Expression Patterns ◽

Functional Characterization ◽

Nac Transcription Factor ◽

Rna Seq ◽

A Genome ◽

Salt And Drought Stress

Abstract Background Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

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RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’

Scientific Reports ◽

10.1038/s41598-021-83372-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chenggen Chu ◽

Shichen Wang ◽

Li Paetzold ◽

Zhen Wang ◽

Kele Hui ◽

...

Keyword(s):

Drought Tolerance ◽

Stress Responses ◽

Expression Patterns ◽

Defense Responses ◽

Wheat Cultivars ◽

Rna Seq ◽

Tolerance Mechanisms ◽

Novel Genes ◽

Altered Expression ◽

Cellular Components

AbstractWheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry–wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry–wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry–wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.

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De novo assembly of Amorpha fruticosa (Amorpha fruticosa L.) transcriptome in response to drought stress provides insight into the tolerance mechanisms

10.21203/rs.2.19443/v1 ◽

2019 ◽

Author(s):

Xinzhu SUN ◽

He LIU ◽

Songmiao HU ◽

Yunwei ZHOU ◽

Qingjie GUAN

Keyword(s):

Salicylic Acid ◽

Drought Stress ◽

Stress Responses ◽

Hormonal Regulation ◽

De Novo ◽

Expression Patterns ◽

Peg 6000 ◽

Amorpha Fruticosa ◽

Drought Tolerant ◽

Wall Signal

Abstract Background Amorpha fruticosa (Amorpha fruticosa L.) is a deciduous shrub that is native to North America and has been introduced to China as an ornamental plant.In order to cultivate drought-tolerant Amorpha fruticosa varieties, it is important to understand the drought-tolerant mechanism of Amorpha fruticosa. Through the changes of the transcriptome of Amorpha fruticosa under drought stress, the mechanism of anti-stress of Amorpha fruticosa could be revealed. Different concentrations of polyethylene glycol-6000 (PEG-6000) was used to simulate drought stress, and transcriptomic analysis was used to reveal the changes of gene expression patterns in Amorpha fruticosa seedlings.Results Results showed that Amorpha fruticosa seedlings were seriously affected by PEG-6000. As for the differently expressed genes (DEGs), most of them were up-regulated. The additional Go and KEGG analysis results showed that DEGs were functionally enriched in cell wall, signal transduction and hormonal regulation related pathways. DEGs like AfSOD, AfHSP, AfTGA, AfbZIP and AfGRX play roles in response to drought stress.Conclusion In conclusion, Amorpha fruticosa seedlings were sensitive to drought, which was different from Amorpha fruticosa tree, and the genes functions in drought stress responses via ABA‐independent pathways. The up-regulation of Salicylic acid signal related DEGs (AfTGA and AfPR-1) indicated that Amorpha fruticosa can resist drought stress through Salicylic acid.

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Transcriptome Analyses in Different Cucumber Cultivars Provide Novel Insights into Drought Stress Responses

International Journal of Molecular Sciences ◽

10.3390/ijms19072067 ◽

2018 ◽

Vol 19 (7) ◽

pp. 2067 ◽

Cited By ~ 4

Author(s):

Min Wang ◽

Biao Jiang ◽

Qingwu Peng ◽

Wenrui Liu ◽

Xiaoming He ◽

...

Keyword(s):

Drought Stress ◽

Rna Sequencing ◽

Stress Responses ◽

Differentially Expressed ◽

Pcr Analysis ◽

Water Deficiency ◽

Sequencing Data ◽

Aba Signal Transduction ◽

Drought Tolerant ◽

Sucrose Biosynthesis

Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and A-16 (drought-sensitive). In our present study, combining the analysis of phenotype, twelve samples of cucumber were carried out a transcriptomic profile by RNA-Seq under normal and water-deficiency conditions, respectively. A total of 1008 transcripts were differentially expressed under normal conditions (466 up-regulated and 542 down-regulated) and 2265 transcripts under drought stress (979 up-regulated and 1286 down-regulated). The significant positive correlation between RNA sequencing data and a qRT-PCR analysis supported the results found. Differentially expressed genes (DEGs) involved in metabolic pathway and biosynthesis of secondary metabolism were significantly changed after drought stress. Several genes, which were related to sucrose biosynthesis (Csa3G784370 and Csa3G149890) and abscisic acid (ABA) signal transduction (Csa4M361820 and Csa6M382950), were specifically induced after 4 days of drought stress. DEGs between the two contrasting cultivars identified in our study provide a novel insight into isolating helpful candidate genes for drought tolerance in cucumber.

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Improving Drought Tolerance in Mungbean (Vigna radiata L. Wilczek): Morpho-Physiological, Biochemical and Molecular Perspectives

Agronomy ◽

10.3390/agronomy11081534 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1534

Author(s):

Chandra Mohan Singh ◽

Poornima Singh ◽

Chandrakant Tiwari ◽

Shalini Purwar ◽

Mukul Kumar ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Crop Production ◽

Mitigation Strategies ◽

Theoretical Research ◽

Whole Genome Sequence ◽

Complex Nature ◽

Drought Tolerant ◽

Breeding Programmes ◽

The Impact

Drought stress is considered a severe threat to crop production. It adversely affects the morpho-physiological, biochemical and molecular functions of the plants, especially in short duration crops like mungbean. In the past few decades, significant progress has been made towards enhancing climate resilience in legumes through classical and next-generation breeding coupled with omics approaches. Various defence mechanisms have been reported as key players in crop adaptation to drought stress. Many researchers have identified potential donors, QTLs/genes and candidate genes associated to drought tolerance-related traits. However, cloning and exploitation of these loci/gene(s) in breeding programmes are still limited. To bridge the gap between theoretical research and practical breeding, we need to reveal the omics-assisted genetic variations associated with drought tolerance in mungbean to tackle this stress. Furthermore, the use of wild relatives in breeding programmes for drought tolerance is also limited and needs to be focused. Even after six years of decoding the whole genome sequence of mungbean, the genome-wide characterization and expression of various gene families and transcriptional factors are still lacking. Due to the complex nature of drought tolerance, it also requires integrating high throughput multi-omics approaches to increase breeding efficiency and genomic selection for rapid genetic gains to develop drought-tolerant mungbean cultivars. This review highlights the impact of drought stress on mungbean and mitigation strategies for breeding high-yielding drought-tolerant mungbean varieties through classical and modern omics technologies.

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Drought Tolerant near Isogenic Lines (NILs) of Pusa 44 Developed through Marker Assisted Introgression of qDTY2.1 and qDTY3.1 Enhances Yield under Reproductive Stage Drought Stress

Agriculture ◽

10.3390/agriculture11010064 ◽

2021 ◽

Vol 11 (1) ◽

pp. 64

Author(s):

Priyanka Dwivedi ◽

Naleeni Ramawat ◽

Gaurav Dhawan ◽

Subbaiyan Gopala Krishnan ◽

Kunnummal Kurungara Vinod ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Grain Quality ◽

Reproductive Stage ◽

Recurrent Parent ◽

Near Isogenic Lines ◽

Improvement Project ◽

Isogenic Lines ◽

Drought Tolerant ◽

Rice Improvement

Reproductive stage drought stress (RSDS) is detrimental for rice, which affects its productivity as well as grain quality. In the present study, we introgressed two major quantitative trait loci (QTLs), namely, qDTY2.1 and qDTY3.1, governing RSDS tolerance in a popular high yielding non-aromatic rice cultivar, Pusa 44, through marker-assisted backcross breeding (MABB). Pusa 44 is highly sensitive to RSDS, which restricts its cultivation across drought-prone environments. Foreground selection was carried out using markers, RM520 for qDTY3.1 and RM 521 for qDTY2.1. Background selection was achieved with 97 polymorphic SSR markers in tandem with phenotypic selection to achieve faster recurrent parent genome (RPG) recovery. Three successive backcrosses followed by three selfings aided RPG recoveries of 98.6% to 99.4% among 31 near isogenic lines (NILs). Fourteen NILs were found to be significantly superior in yield and grain quality under RSDS with higher drought tolerance efficiency (DTE) than Pusa 44. Among these, the evaluation of two promising NILs in the multilocational trial during Kharif 2019 showed that they were significantly superior to Pusa 44 under reproductive stage drought stress, while performing on par with Pusa 44 under normal irrigated conditions. These di-QTL pyramided drought-tolerant NILs are in the final stages of testing the All India Coordinated Rice Improvement Project varietal trials for cultivar release. Alternately, the elite drought-tolerant Pusa 44 NILs will serve as an invaluable source of drought tolerance in rice improvement.

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