scholarly journals Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 596 ◽  
Author(s):  
Behnam Derakhshani ◽  
Habtamu Ayalew ◽  
Kohei Mishina ◽  
Tsuyoshi Tanaka ◽  
Yoshihiro Kawahara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Water Stress ◽  
Protein Function ◽  
High Salinity ◽  
Expression Patterns ◽  
Natural Environments ◽  
Homoeologous Gene ◽  
Water Stress Tolerance ◽  
Homoeologous Genes ◽  
Response To Water

Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.

scholarly journals The Combination of Abscisic Acid (ABA) and Water Stress Regulates the Epicuticular Wax Metabolism and Cuticle Properties of Detached Citrus Fruit

2021 ◽  
Vol 22 (19) ◽  
pp. 10242
Author(s):  
Paco Romero ◽  
María Teresa Lafuente
Keyword(s):  
Abscisic Acid ◽  
Water Stress ◽  
Expression Patterns ◽  
Citrus Fruit ◽  
Epicuticular Wax ◽  
Storage Duration ◽  
Metabolism Regulation ◽  
Response To Water ◽  
Layer Composition ◽  
Wax Load

The phytohormone abscisic acid (ABA) is a major regulator of fruit response to water stress, and may influence cuticle properties and wax layer composition during fruit ripening. This study investigates the effects of ABA on epicuticular wax metabolism regulation in a citrus fruit cultivar with low ABA levels, called Pinalate (Citrus sinensis L. Osbeck), and how this relationship is influenced by water stress after detachment. Harvested ABA-treated fruit were exposed to water stress by storing them at low (30–35%) relative humidity. The total epicuticular wax load rose after fruit detachment, which ABA application decreased earlier and more markedly during fruit-dehydrating storage. ABA treatment changed the abundance of the separated wax fractions and the contents of most individual components, which reveals dependence on the exposure to postharvest water stress and different trends depending on storage duration. A correlation analysis supported these responses, which mostly fitted the expression patterns of the key genes involved in wax biosynthesis and transport. A cluster analysis indicated that storage duration is an important factor for the exogenous ABA influence and the postharvest environment on epicuticular wax composition, cuticle properties and fruit physiology. Dynamic ABA-mediated reconfiguration of wax metabolism is influenced by fruit exposure to water stress conditions.

Effect of Different CO2 Regimes on the Induction of Crassulacean Acid Metabolism in Mesembryanthemum crystallinum L

1979 ◽  
Vol 6 (6) ◽  
pp. 589 ◽  
Author(s):  
K Winter
Keyword(s):  
Water Stress ◽  
Phosphoenolpyruvate Carboxylase ◽  
Crassulacean Acid Metabolism ◽  
Acid Metabolism ◽  
High Salinity ◽  
Stomatal Closure ◽  
Initial Step ◽  
Mesembryanthemum Crystallinum ◽  
Initial Event ◽  
Response To Water

Induction of crassulacean acid metabolism (CAM) in Mesembryanthemum crystallinum in response to high salinity was studied in plants grown in different CO2 regimes to determine whether the induction of CAM could be controlled by CO2 supply in the light and dark; a possible consequence of stomatal closure in response to water stress. The activity of extractable phosphoenolpyruvate carboxylase (EC 4.1.1.31) and the nocturnal change in malate content were followed at frequent intervals after onset of the treatments. The results suggest that the initial event during the induction of CAM is a change in the biochemical apparatus, indicated by the activity of phosphoenolpyruvate carboxylase, which then leads to the day/night fluctuations of malate synthesis typical of CAM. This initial step is not controlled by the availability of CO2 in the light or dark.

scholarly journals Predicting bacterial growth conditions from mRNA and protein abundances

2018 ◽  
Author(s):  
Mehmet U. Caglar ◽  
Adam J. Hockenberry ◽  
Claus O. Wilke
Keyword(s):  
Gene Expression ◽  
Species Interactions ◽  
Low Cost ◽  
Expression Patterns ◽  
Single Species ◽  
Growth Conditions ◽  
Environmental Variable ◽  
Training Data ◽  
Specific Gene ◽  
Natural Environments

AbstractCells respond to changing nutrient availability and external stresses by altering the expression of individual genes. Condition-specific gene expression patterns may provide a promising and low-cost route to quantifying the presence of various small molecules, toxins, or species-interactions in natural environments. However, whether gene expression signatures alone can predict individual environmental growth conditions remains an open question. Here, we used machine learning to predict 16 closely-related growth conditions using 155 datasets of E. coli transcript and protein abundances. We show that models are able to discriminate between different environmental features with a relatively high degree of accuracy. We observed a small but significant increase in model accuracy by combining transcriptome and proteome-level data, and we show that stationary phase conditions are typically more difficult to distinguish from one another than conditions under exponential growth. Nevertheless, with sufficient training data, gene expression measurements from a single species are capable of distinguishing between environmental conditions that are separated by a single environmental variable.

scholarly journals Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2664
Author(s):  
Maria Angeles Decena ◽  
Sergio Gálvez-Rojas ◽  
Federico Agostini ◽  
Ruben Sancho ◽  
Bruno Contreras-Moreira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Water Stress ◽  
Comparative Genomics ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Genomic Sequence ◽  
Grass Species ◽  
Phenotypic Traits ◽  
Water Stress Tolerance ◽  
Dehydrin Genes

Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus’ flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses.

Gene Expression Profiles of Response to Water Stress at the Jointing Stage in Wheat

2010 ◽  
Vol 9 (3) ◽  
pp. 325-330 ◽  
Author(s):  
Jun-feng SHI ◽  
Xin-guo MAO ◽  
Rui-lian JING ◽  
Xiao-bin PANG ◽  
Yu-guo WANG ◽  
...  
Keyword(s):  
Gene Expression ◽  
Water Stress ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Jointing Stage ◽  
Response To Water

scholarly journals Transcriptome Profiles of Contrasting Potato (Solanum tuberosum L.) Genotypes Under Water Stress

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 848 ◽  
Author(s):  
Macarena Barra ◽  
Claudio Meneses ◽  
Stephanie Riquelme ◽  
Manuel Pinto ◽  
Martin Lagüe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Water Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Agricultural Research ◽  
Solanum Tuberosum L ◽  
Differentially Expressed ◽  
Polyamine Biosynthesis ◽  
Water Stress Tolerance ◽  
Expression Of Genes

The potato is susceptible to water stress at all stages of development. We examined four clones of tetraploid potato, Cardinal, Desirée, Clone 37 FB, and Mije, from the germplasm bank of the National Institute of Agricultural Research (INIA) in Chile. Water stress was applied by suspending irrigation at the beginning of tuberization. Stomatal conductance, and tuber and plant fresh and dry weight were used to categorize water stress tolerance. Cardinal had a high susceptibility to water stress. Desirée was less susceptible than Cardinal and had some characteristics of tolerance. Mije had moderate tolerance and Clone 37 FB had high tolerance. Differential gene expression in leaves from plants with and without water stress were examined using transcriptome sequencing. Water stress-susceptible Cardinal had the fewest differentially expressed genes at 101, compared to Desirée at 1867, Clone 37 FB at 1179, and Mije at 1010. Water stress tolerance was associated with upregulation of the expression of transcription factor genes and genes involved in osmolyte and polyamine biosynthesis. Increased expression of genes encoding late embryogenesis abundant (LEA) and dehydrin proteins along with decreased expression of genes involved in nitrate assimilation and amino acid metabolism were found for clones showing water stress tolerance. The results also show that a water deficit was associated with reduced biotic stress responses. Additionally, heat shock protein genes were differentially expressed in all clones except for highly susceptible Cardinal. Together, the gene expression study demonstrates variation in the molecular pathways and biological processes in response to water stress contributing to tolerance and susceptibility.

scholarly journals The ALBA RNA-binding proteins function redundantly to promote growth and flowering in Arabidopsis

2019 ◽  
Author(s):  
Naiqi Wang ◽  
Meachery Jalajakumari ◽  
Thomas Miller ◽  
Mohsen Asadi ◽  
Anthony A Millar
Keyword(s):  
Gene Expression ◽  
Protein Function ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Short Form ◽  
Expression Patterns ◽  
Wild Type ◽  
Long Form ◽  
Mrna Binding

AbstractRNA-binding proteins (RBPs) are critical regulators of gene expression, but have been poorly studied relative to other classes of gene regulators. Recently, mRNA-interactome capture identified many Arabidopsis RBPs of unknown function, including a family of ALBA domain containing proteins. Arabidopsis has three short-form ALBA homologues (ALBA1-3) and three long-form ALBA homologues (ALBA4-6), both of which are conserved throughout the plant kingdom. Despite this ancient origin, ALBA-GUS translational fusions of ALBA1, ALBA2, ALBA4, and ALBA5 had indistinguishable expression patterns, all being preferentially expressed in young, rapidly dividing tissues. Likewise, all four ALBA proteins had indistinguishable ALBA-GFP subcellular localizations in roots, all being preferentially located to the cytoplasm, consistent with being mRNA-binding. Genetic analysis demonstrated redundancy within the long-form ALBA family members; in contrast to single alba mutants that all appeared wild-type, a triple alba456 mutant had slower rosette growth and a strong delay in flowering-time. RNA-sequencing found most differentially expressed genes in alba456 were related to metabolism, not development. Additionally, changes to the alba456 transcriptome were subtle, suggesting ALBA4-6 participates in a process that does not strongly affect transcriptome composition. Together, our findings demonstrate that ALBA protein function is highly redundant, and is essential for proper growth and flowering in Arabidopsis.HighlightThe RNA-binding ALBA proteins have indistinguishable expression patterns and subcellular localizations in Arabidopsis, acting redundantly to promote growth and flowering via a mechanism that does not strongly affect transcriptome composition.

Tolerance at the genetic level of the brine shrimp Artemia salina to a wide range of salinity

2020 ◽  
Author(s):  
JunMo Lee ◽  
Jong Soo Park
Keyword(s):  
Gene Expression ◽  
Brine Shrimp ◽  
High Salinity ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Artemia Salina ◽  
Gene Expression Patterns ◽  
Organic Osmolytes ◽  
High Quality ◽  
Genetic Level

Abstract Background: The brine shrimp Artemia salina can thrive in a variety of salinities and is commonly distributed in natural hypersaline lakes and solar salterns. The zooplankter A. salina proves to be a filter feeder, consuming the alga Dunaliella and prokaryotes and plays a critical role in the hypersaline food web. However, the high salinity adaptation mechanisms of A. salina remain poorly understood through transcriptome analysis. Here, we examined the gene expression patterns of A. salina adults that were salt-adapted for 2–4 weeks at five salinities (35, 50, 100, 150, and 230 psu), and generated long-read isoform sequencing (IsoSeq) data to construct a high-quality transcriptome assembly of A. salina. The patterns of A. salina along the salinity gradient provide evidence for halotolerant and euryhaline adaptations at the genetic level. Results: We confirmed that the activity of sodium/potassium ATPase was up-regulated at the genetic level in high salinity waters. Interestingly, genes related to beta-mannosidase and mannose activities were also up-regulated, suggesting that mannose and mannose derivatives may be accumulated as organic osmolytes. Alternatively, considering that glucose and galactose-related activities were suppressed at high salinities, mannose may be the primary sugar involved in the glycolytic pathway under such conditions. This result further supports the theory that mannose is the main energy source used by A. salina in highly saline environments. The gene expression patterns of A. salina may also be affected by increased thickness of the cuticle, increased numbers of mitochondria, and low dissolved oxygen in high salinity waters. Furthermore, the cellular response of A. salina to acclimation to intermediate salinities depends on the number and type of genes expressed; differential expression patterns are likely to fluctuate at the population level. Conclusions: Our results provide a high-quality transcriptome assembly of the cosmopolitan brine shrimp Artemia salina at five different salinities (35, 50, 100, 150, and 230 psu) for the first time. The gene expression patterns of salt-adapted A. salina display greater osmoregulation process complexity than we thought. Furthermore, A. salina represents a potential model organism to study locally adapted populations at various salinities.

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