scholarly journals New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Éderson Akio Kido ◽  
José Ribamar Costa Ferreira Neto ◽  
Roberta Lane de Oliveira Silva ◽  
Valesca Pandolfi ◽  
Ana Carolina Ribeiro Guimarães ◽  
...  
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Present Report ◽  
Transcriptome Profiling ◽  
Water Deficit Stress ◽  
New Genes ◽  
Drought Tolerant ◽  
Blastn Analysis ◽  
Root Tissues ◽  
Solexa Sequencing Technology

In the scope of the present work, four SuperSAGE libraries have been generated, using bulked root tissues from four drought-tolerant accessions as compared with four bulked sensitive genotypes, aiming to generate a panel of differentially expressed stress-responsive genes. Both groups were submitted to 24 hours of water deficit stress. The SuperSAGE libraries produced 8,787,315 tags (26 bp) that, after exclusion of singlets, allowed the identification of 205,975 unitags. Most relevant BlastN matches comprised 567,420 tags, regarding 75,404 unitags with 164,860 different ESTs. To optimize the annotation efficiency, the Gene Ontology (GO) categorization was carried out for 186,191 ESTs (BlastN against Uniprot-SwissProt), permitting the categorization of 118,208 ESTs (63.5%). In an attempt to elect a group of the best tags to be validated by RTqPCR, the GO categorization of the tag-related ESTs allowed thein silicoidentification of 213 upregulated unitags responding basically to abiotic stresses, from which 145 presented no hits after BlastN analysis, probably concerning new genes still uncovered in previous studies. The present report analyzes the sugarcane transcriptome under drought stress, using a combination of high-throughput transcriptome profiling by SuperSAGE with the Solexa sequencing technology, allowing the identification of potential target genes during the stress response.

Transcriptomic response in foliar and root tissues of a drought-tolerant Eucalyptus globulus genotype under drought stress

Trees ◽  
2021 ◽  
Author(s):  
José Luis Ulloa ◽  
Paula Aguayo ◽  
Daniel Conejera ◽  
Rafael Rubilar ◽  
Claudio Balocchi ◽  
...  
Keyword(s):  
Drought Stress ◽  
Eucalyptus Globulus ◽  
Transcriptomic Response ◽  
Drought Tolerant ◽  
Root Tissues

scholarly journals Transcriptome profiling of faba bean (Vicia faba L.) drought-tolerant variety hassawi-2 under drought stress using RNA sequencing

2019 ◽  
Vol 39 ◽  
pp. 15-29 ◽  
Author(s):  
Muhammad Altaf Khan ◽  
Salem S. Alghamdi ◽  
Megahed H. Ammar ◽  
Qiwei Sun ◽  
Fei Teng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Vicia Faba ◽  
Faba Bean ◽  
Transcriptome Profiling ◽  
Drought Tolerant ◽  
Vicia Faba L ◽  
Tolerant Variety

Bm-miR172c-5p regulates lignin biosynthesis and secondary xylem thickness by altering Ferulate 5 hydroxylase gene in Bacopa monnieri

2021 ◽  
Author(s):  
Gajendra Singh Jeena ◽  
Ashutosh Joshi ◽  
Rakesh Kumar Shukla
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Secondary Xylem ◽  
Lignin Biosynthesis ◽  
Small Rna Sequencing ◽  
Cleavage Sites ◽  
Environmental Condition ◽  
Cycloartenol Synthase ◽  
Root Tissues

Abstract MicroRNAs (miRNAs) are small non-coding, endogenous RNAs containing 20–24 nucleotides that regulate the expression of target genes involved in various plant processes. A total 1429 conserved miRNA belonging to 95 conserved miRNA families and 12 novel miRNAs were identified from B. monnieri using small RNA sequencing. The Bm-miRNA target transcripts related to the secondary metabolism were further selected for validation. The Bm-miRNA expression in shoot and root tissues were negatively correlated with their target transcripts. The Bm-miRNA cleavage sites were mapped within the coding or untranslated (UTR) region as depicted by the modified RLM-RACE. In the present study, we validate three miRNA targets, including Asparagine synthetase, Cycloartenol synthase, and Ferulate 5 hydroxylase and elucidate the regulatory role of Bm-miR172c-5p, which cleaves the F5H gene involved in the lignin biosynthesis. Overexpression of Bm-miR172c-5p precursor in B. monnieri suppress F5H gene, leading to reduced lignification and secondary xylem thickness under control and drought stress. In contrast, overexpression of target mimics (eTMs) showed enhanced lignification and secondary xylem thickness leading to better physiological response under drought stress. Taken together, we suggest that Bm-miRNA172c-5p might be a key player in maintaining the native phenotype of B. monnieri under control and different environmental condition.

scholarly journals Integrative Analysis of Transcriptomic and Physiological Reveals Drought Adaption Strategies in Different Maize Genotypes

2021 ◽  
Author(s):  
Yifan Wang ◽  
Xi Wu ◽  
Hongjie Li ◽  
Miaoyi Hao ◽  
Renhe Zhang
Keyword(s):  
Drought Stress ◽  
Protein Modification ◽  
Net Photosynthesis ◽  
Transcriptome Profiling ◽  
Enzymatic Antioxidants ◽  
Maize Productivity ◽  
Drought Tolerant ◽  
Genes Expression ◽  
Maize Varieties ◽  
Drought Adaption

Abstract Background: Drought is an environmental stress that adversely affects maize productivity. However, drought adaption strategies of different maize varieties are not fully clear at the transcriptomic level. In the paper, drought-sensitive SD902 and -resistant SD609 varieties were analyzed to explore transcriptional and physiological alterations to drought stress. Results: The higher SOD, CAT, GSH enzymatic antioxidants, stomatal conductance, transpiration, net photosynthesis rate suggested better performance of SD609 than SD902 variety under drought stress. In transcriptome profiling, a total of 8985 and 7305 difference expression genes (DEGs) were identified in SD902 and SD609 respectively. These genes were overall involved in antioxidation reduce, osmotic adjustment, protein modification (e.g. HSP and chaperone protein), photosynthesis, phytohormone (e.g. ABA, IAA, ethylene), transcription factors (TFs) (e.g. ERF, WRKY, NAC and bZIP) and MAPK (MAPK1/8, MKK4/9 and MKKK17) cascade. Among them, the upregulated genes significantly correlated with stress adjustment, HSPs and chaperone functions might better reduce drought-induced damage in both SD902 and especially SD609. The higher genes expression of IAA, ethylene and electron transfer in SD609 may be closely related to drought-tolerant performance than SD902 plants. Moreover, the misregulation of TFs, MAPK and ABA signaling would appear vital to explain the various sensitivity to drought in both varieties. Conclusion: The more drought-tolerant SD609 presented a beneficial and significantly higher genes expression of stress protection, IAA transduction, photosynthesis compared with drought-sensitive SD902 variety. Our findings provide vital insights into the molecular signatures underpinning drought resistance in maize.

scholarly journals Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley

2020 ◽  
Vol 21 (8) ◽  
pp. 2795
Author(s):  
Cheng-Wei Qiu ◽  
Li Liu ◽  
Xue Feng ◽  
Peng-Fei Hao ◽  
Xiaoyan He ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Target Genes ◽  
Wild Barley ◽  
Expression Profiles ◽  
Tibetan Wild Barley ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Barley Genotypes

Drought stress is a major obstacle to agricultural production. Tibetan wild barley with rich genetic diversity is useful for drought-tolerant improvement of cereals. MicroRNAs (miRNAs) play critical roles in controlling gene expression in response to various environment perturbations in plants. However, the genome-wide expression profiles of miRNAs and their targets in response to drought stress are largely unknown in wild barley. In this study, a polyethylene glycol (PEG) induced drought stress hydroponic experiment was performed, and the expression profiles of miRNAs from the roots of two contrasting Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one cultivated barley Tadmor (drought-tolerant) generated by high-throughput sequencing were compared. There were 69 conserved miRNAs and 1574 novel miRNAs in the dataset of three genotypes under control and drought conditions. Among them, seven conserved miRNAs and 36 novel miRNAs showed significantly genotype-specific expression patterns in response to drought stress. And 12 miRNAs were further regarded as drought tolerant associated miRNAs in XZ5, which mostly participate in gene expression, metabolism, signaling and transportation, suggesting that they and their target genes play important roles in plant drought tolerance. This is the first comparation study on the miRNA transcriptome in the roots of two Tibetan wild barley genotypes differing in drought tolerance and one drought tolerant cultivar in response to PEG treatment. Further results revealed the candidate drought tolerant miRNAs and target genes in the miRNA regulation mechanism in wild barley under drought stress. Our findings provide valuable understandings for the functional characterization of miRNAs in drought tolerance.

Mitigation of drought stress in maize through inoculation with drought tolerant ACC deaminase containing PGPR under axenic conditions

2019 ◽  
Vol 52 (1) ◽  
Author(s):  
Subhan Danish ◽  
Muhammad Zafar-Ul-Hye ◽  
Shahid Hussain ◽  
Muhammad Riaz ◽  
Muhammad Farooq Qayyum
Keyword(s):  
Drought Stress ◽  
Acc Deaminase ◽  
Drought Tolerant ◽  
Axenic Conditions

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

scholarly journals Flavonoids improve drought tolerance of maize seedlings by regulating the homeostasis of reactive oxygen species

2021 ◽  
Author(s):  
Baozhu Li ◽  
Ruonan Fan ◽  
Guiling Sun ◽  
Ting Sun ◽  
Yanting Fan ◽  
...  
Keyword(s):  
Free Radicals ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Infrared Imaging ◽  
Oxygen Free Radicals ◽  
Transcriptome Profiling ◽  
Far Infrared ◽  
Drought Treatment ◽  
Physiological Characterization ◽  
Oxidative Damages

Abstract Background and aims As drought threatens the yield and quality of maize (Zea mays L.), it is important to dissect the molecular basis of maize drought tolerance. Flavonoids, participate in the scavenging of oxygen free radicals and alleviate stress-induced oxidative damages. This study aims to dissect the function of flavonoids in the improvement of maize drought tolerance. Methods Using far-infrared imaging screening, we previously isolated a drought overly insensitivity (doi) mutant from an ethyl methanesulfonate (EMS)-mutagenized maize library and designated it as doi57. In this study, we performed a physiological characterization and transcriptome profiling of doi57 in comparison to corresponding wild-type B73 under drought stress. Results Under drought stress, doi57 seedlings displayed lower leaf-surface temperature (LST), faster water loss, and better performance in growth than B73. Transcriptome analysis reveals that key genes involved in flavonoid biosynthesis are enriched among differentially expressed genes in doi57. In line with these results, more flavonols and less hydrogen peroxide (H2O2) were accumulated in guard cells of doi57 than in those of B73 with the decrease of soil water content (SWC). Moreover, the capacity determined from doi57 seedling extracts to scavenge oxygen free radicals was more effective than that of B73 under the drought treatment. Additionally, doi57 seedlings had higher photosynthetic rates, stomatal conductance, transpiration rates, and water use efficiency than B73 exposed to drought stress, resulting in high biomass and greater root/shoot ratios in doi57 mutant plants. Conclusion Flavonoids may facilitate maize seedling drought tolerance by lowering drought-induced oxidative damage as well regulating stomatal movement.

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