scholarly journals Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247181
Author(s):  
Jiguang Li ◽  
Yanlan Wang ◽  
Liqun Wang ◽  
Jianyu Zhu ◽  
Jing Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Finger Millet ◽  
Unsaturated Fatty Acids ◽  
Comparison Group ◽  
Eleusine Coracana ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Carbohydrate Binding ◽  
Oxidoreductase Activity

Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

scholarly journals Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Z. Y. Su ◽  
J. J. Powell ◽  
S. Gao ◽  
M. Zhou ◽  
C. Liu
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Crown Rot ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Drought Treatment ◽  
Crop Species ◽  
Fusarium Crown Rot ◽  
Important Relationship ◽  
The Impact

Abstract Background Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops. Results In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection. Conclusions Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

scholarly journals Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat

2020 ◽  
Author(s):  
Xiangchi Zhang ◽  
Weidan Lu ◽  
Xiaoli Wang ◽  
Bin Ma ◽  
Kaiyong Fu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Winter Wheat ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Phosphorus Level ◽  
Root Tips ◽  
Percentage Content ◽  
Low Phosphorus

Abstract Phosphorus stress and drought stress are common abiotic stresses. In this study, two winter wheat “Xindong20” and “Xindong23” were solution cultured and then treated with drought stress under conventional phosphorus level (CP: 1.0 mmol/L) and low phosphorus level (LP: 0.05 mmol /L), respectively. The results showed that with the increase of drought stress, the LP application was more conducive to the growth of root tips, length, forks, surfarea and root vitality of wheat. Under the LP treatment, the total phosphorus content of root at rewatered 3d was increased by 94.2% in Xindong20 wheat and decreased by 48.9% in Xindong23 wheat, compared with their respective samples at drought 0d. The LP treatment increased the percentage content of K and decreased the P and Ca percentage content. However, under CP treatment, the percentage content of Zn after rewatered 3 days were increased, compared with drought 7d. Based on the GeneChip analysis of root samples from drought 7d, the microarray results showed that 4577 and 202 differentially expressed genes were detected from Xindong20 and Xindong23, respectively. Among them, 89.9% of differentially expressed genes were involved in organelles and vesicles in Xindong20, and 69.8% were involved in genes encoding root anatomical structure, respiratory chain, electron transport chain, ion transport and enzyme activity in Xindong23. Therefore, the supply of low phosphorus has more effects on the drought tolerance of wheat, and the wheat with different drought tolerance has different regulatory genes. The higher drought-tolerant wheat has more genes up-regulation in response to drought stress.

scholarly journals Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton

2021 ◽  
Vol 22 (2) ◽  
pp. 898
Author(s):  
Muhammad Sajjad ◽  
Xi Wei ◽  
Lisen Liu ◽  
Fuguang Li ◽  
Xiaoyang Ge
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Plant Growth ◽  
Growth And Development ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Regulatory Pathways ◽  
Vascular Growth

Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.

scholarly journals Mycorrhiza Fungus Rhizophagus intraradices Mediates Drought Tolerance in Eleusine coracana Seedlings

2018 ◽  
Author(s):  
Jaagriti Tyagi ◽  
Neeraj Shrivastava ◽  
A. K. Sharma ◽  
Ajit Varma ◽  
Ramesh Namdeo Pudake
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Finger Millet ◽  
Soluble Sugars ◽  
Leaf Tissue ◽  
Am Fungi ◽  
Mycorrhizal Symbiosis ◽  
Severe Drought ◽  
Rhizophagus Intraradices

Under abiotic stress conditions, arbuscular mycorrhizal (AM) fungi help plants by improving nutrient and water uptake. Finger millet is an arid crop having soils with poor water holding capacity. Therefore, it is difficult for the plants to obtain water and mineral nutrients from the soil to sustain life. To understand the role of mycorrhizal symbiosis in water and mineral up-take from the soil, we studied the role of Rhizophagus intraradices colonization and its beneficial role for drought stress tolerance in finger millet seedling. Under severe drought stress condition, AM inoculation led to the significant increase in plant growth (7%), phosphorus, and chlorophyll content (29%). Also, the level of osmolytes including proline and soluble sugars were found in higher quantities in AM inoculated seedlings under drought stress. Under water stress, the lipid peroxidation in leaves of mycorrhized seedlings was reduced by 29%. The flavonoid content of roots in AM colonized seedlings was found 16% higher compared to the control, whereas the leaves were accumulated more phenol. Compared to the control, ascorbate level was found to be 25% higher in leaf tissue of AM inoculated seedlings. Moreover, glutathione (GSH) level was increased in mycorrhiza inoculated seedlings with a maximum increment of 182% under severe stress. The results demonstrated that AM provided drought tolerance to the finger millet seedlings through a stronger root system, greater photosynthetic efficiency, a more efficient antioxidant system and improved osmoregulation.

scholarly journals Comparative Analysis of Alfalfa (Medicago Sativa L.) Seedling Transcriptomes Reveals Genotype-specific Drought Tolerance Mechanisms

2020 ◽  
Author(s):  
Qiaoli Ma ◽  
Xing Xu ◽  
Yingzhong Xie ◽  
Wenjing Wang ◽  
Lijuan Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Differentially Expressed Genes ◽  
Amine Oxidase ◽  
Abiotic Factors ◽  
Resistance Breeding ◽  
Complex Trait ◽  
Fatty Acyl ◽  
Differentially Expressed ◽  
Cell Membrane Stability

Abstract BackgroundDrought is one of the main abiotic factors that affect alfalfa yield. The identification of genes that control this complex trait can provide important insights for alfalfa breeding. However, little is known about how alfalfa responds and adapts to drought stress, particularly in cultivars of differing drought tolerance. ResultsIn this study, the drought-tolerant cultivar Dryland ‘DT’ and the drought-sensitive cultivar WL343HQ ‘DS’ were used to characterize leaf and root physiological responses and transcriptional changes in response to water deficit. Under drought stress, Dryland roots (DTR) showed more differentially expressed genes than WL343HQ roots (DSR), whereas WL343HQ leaves (DSL) showed more differentially expressed genes than Dryland leaves (DTL). Many of these genes were involved in stress-related pathways, carbohydrate metabolism, and lignin and wax biosynthesis, which may have improved the drought tolerance of alfalfa. We also observed that several genes related to ABA metabolism, root elongation, peroxidase activity, cell membrane stability, ubiquitination, and genetic processing responded to drought stress in alfalfa. We highlighted several candidate genes, including sucrose synthase, xylan 1,4-beta-xylosidase, primary-amine oxidase, and alcohol-forming fatty acyl-CoA reductase, for future studies on drought stress resistance in alfalfa and other plant species. ConclusionsIn summary, our results reveal the unique drought adaptation and resistance characteristics of two alfalfa genotypes. These findings, which may be valuable for drought resistance breeding, warrant further gene functional analysis to augment currently available information and to clarify the drought stress regulatory mechanisms of alfalfa and other plants.

scholarly journals Do Species Mount Different Genetic Responses to Acute Drought Stress Across an Ecological Gradient? 

2020 ◽  
Author(s):  
Jessica Kay Devitt ◽  
Albert Chung ◽  
John J. Schenk
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Target Genes ◽  
Differentially Expressed ◽  
Tissue Type ◽  
Model Organisms ◽  
Drought Response ◽  
Delayed Senescence ◽  
Tissue Responses ◽  
Genetic Responses

Abstract Background: How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in non-model organisms are unknown. We investigated this question in Mentzelia section Bartonia (Loasaceae), which occurs throughout western North America, including arid lands. To better understand the genetic responses to drought stress among species that occur in different habitats, the gene expression levels of three species from the genus Mentzelia that occur across a precipitation gradient were compared. Two de novo reference transcriptomes were generated and annotated. Leaf and root tissues were collected from control and drought shocked plants and compared to one another for differential expression. A target-gene approach was also implemented to better understand how drought-related genes from model and crop species function in non-model systems.Results: When comparing the drought-shock treatment plants to their respective control plants, we identified 165 differentially expressed clusters across all three species. Differentially expressed genes including those associated with water movement, photosynthesis, and genes that delayed senescence. The transcriptome profiling approach was coupled with a target genes approach that measured expression of 90 genes associated with drought tolerance in model organisms. Comparing differentially expressed genes with a log-fold values of 2 or greater between species and tissue types showed significant differences in drought response. In pariwise comparisons, species that occurred in drier environments differentially expressed greater genes in leaves when drought shocked than those from wetter environments, but expression in the roots mostly produced opposite results. Conclusions: Arid-adapted species mounted greater genetic responses compared to the temperate species, with differences in leaf and root tissue responses. Target genes revealed differences and similarities between functional processes within Mentzelia and other plant groups. Differences in drought response depending on tissue type suggests that genetic and physiological responses occur within one tissue type and not the other, and tissue responses could be evolving at different rates. We determined that drought tolerance is enhanced through pathways of delayed senescence and that genetic responses were tissue and habitat specific.

scholarly journals Physiological characterization of finger millet (Eleusine coracana L.) for drought tolerance

2017 ◽  
Vol 13 (2) ◽  
pp. 403-409
Author(s):  
S. MOHAN KUMAR ◽  
H.R. MANU KUMAR ◽  
S.J. PRASHANTH ◽  
SHAILAJA HITTALAMANI ◽  
M. UDAYA KUMAR
Keyword(s):  
Drought Tolerance ◽  
Finger Millet ◽  
Eleusine Coracana ◽  
Physiological Characterization

scholarly journals Comparative Proteomics Analysis of the Seedling Root Response of Drought-sensitive and Drought-tolerant Maize Varieties to Drought Stress

2019 ◽  
Vol 20 (11) ◽  
pp. 2793 ◽  
Author(s):  
Wenjing Zeng ◽  
Yunling Peng ◽  
Xiaoqiang Zhao ◽  
Boyang Wu ◽  
Fenqi Chen ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Molecular Mechanisms ◽  
Mrna Level ◽  
Differentially Expressed ◽  
Water Retention Capacity ◽  
Coding Region ◽  
Retention Capacity ◽  
Drought Tolerant ◽  
Maize Varieties

The growth and development of maize roots are closely related to drought tolerance. In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, the isobaric tags for relative and absolute quantitation (iTRAQ) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% polyethylene glycol 6000 (PEG 6000)-simulated drought stress. We identified a total of 7723 differentially expressed proteins (DEPs), 1243 were significantly differentially expressed in Chang 7-2 following drought stress, 572 of which were up-regulated and 671 were down-regulated; 419 DEPs were identified in TS141, 172 of which were up-regulated and 247 were down-regulated. In Chang 7-2, the DEPs were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the DEPs were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism. Compared with TS141, the higher drought tolerance of Chang 7-2 root system was attributed to a stronger water retention capacity; the synergistic effect of antioxidant enzymes; the strengthen cell wall; the osmotic stabilization of plasma membrane proteins; the effectiveness of recycling amino acid; and an improvement in the degree of lignification. The common mechanisms of the drought stress response between the two varieties included: The promotion of enzymes in the glycolysis/gluconeogenesis pathway; cross-protection against the toxicity of aldehydes and ammonia; maintenance of the cell membrane stability. Based on the proteome sequencing information, the coding region sequences of eight DEP-related genes were analyzed at the mRNA level by quantitative real-time PCR (qRT-PCR). The findings of this study can inform the future breeding of drought-tolerant maize varieties.

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