Profiles of phenolic secondary metabolites in plants of barley (Hordeum vulgare L.)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Acquity UPLC PDA, Bruker Daltonics esquire 3000
SUBMITTER: Anna Piasecka
PROVIDER: MTBLS52 | MetaboLights | 2014-11-20
REPOSITORIES: MetaboLights
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Project description:Background: Drought stress is the major environmental stress that affects plant growth and productivity. It triggers in plants a wide range of responses detectable at different scales: molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, explore the subtle differences existing in gene expression of drought sensitive and drought tolerant genotypes allows to identify drought-related genes that could be used for selection of drought tolerance traits. Genome-wide RNA-Seq technology was used to compare the drought response of two sorghum genotypes characterized by contrasting water use efficiency. Results: the physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 previously studied. The expression of drought-related genes was more abundant in the sensitive genotype IS20351 compared to the tolerant IS22330. The Gene Ontology enrichment highlighted a massive increase in transcript abundance in “response to stress” and “abiotic stimulus”, “oxidation-reduction reaction” in the sensitive genotype IS20351 under drought stress. “Antioxidant” and “secondary metabolism”, “photosynthesis and carbon fixation process”, “lipids” and “carbon metabolism” were the pathways most affected by drought in the sensitive genotype IS20351. The sensitive genotype IS20351 showed under well-watered conditions a lower constitutive expression level of “secondary metabolic process” (GO:0019748) and “glutathione transferase activity” (GO:000004364). Conclusions: RNA-Seq analysis revealed to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. The transcriptomic results supported all the physiological measurements and were crucial to clarify the tolerance of the two genotypes studied. The connection between the differential gene expression and the physiological response to drought states unequivocally the drought tolerance of the genotype IS22330 and the strategy adopted to cope with drought stress.
2016-04-27 | GSE80699 | GEO
Project description:Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.
2019-12-31 | GSE123381 | GEO
Project description:Drought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large scale circRNA profiling identified 2174 and 1354 high-confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought-associated circRNA hosting genes were involved in conserved or species-specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA-hosting genes were enriched for SNPs associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought-tolerant maize. Additionally, the expression levels of circRNAs derived from drought-responsible genes encoding calcium-dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward-rectifying K+-channel) were hypersensitive to ABA, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidences highlighting the universal molecular mechanisms involved in plant drought tolerance.
2018-12-25 | GSE124340 | GEO
Project description:As a major plant abiotic stress, drought stress suppresses crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance becomes a great challenge in drought-resistant crop breeding. Several phytohormones have been reported to participate in plant drought response, including gibberellin (GA), which also plays an important role in plant growth and development. Using CRISPR technology, we constructed the null mutant of ZmGA20ox3, a key enzyme in GA biosynthesis. The null mutant plants show lower plant height and ear height with no yield loss under the normal condition than wild-type plants. Transcriptome analysis revealed that genes affected by ZmGA20ox3 were enriched in signal transduction and stress response processes. In addition to the decrease of GA, a significant increase of ABA and JA level were also detected in mutant plants. Compared with wild-type plants, the growth and ASI of mutant plants were less affected, and the yield loss was also reduced under drought conditions. These results suggest a potential role of ZmGA20ox3 in maize drought response. Our result shows that regulating GA biosynthesis is applicable for maize drought-resistant breeding.
2024-04-10 | GSE229138 | GEO
Project description:Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought tolerant) or 125AA (drought sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100 % veraison. The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signalling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA concerning genes related to jasmonate, phenylpropanoid metabolism and PR-proteins. The data also suggests a link between jasmonate and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and jasmonate are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties.
2015-03-19 | GSE66391 | GEO
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize. In two independent experiments, we generate maize gene expression profiles during drought stress and re-watering through comparing genome-wide expression patterns of drought stress treatment and re-watering treatment by using 17,555 Affymetrix maize whole genome array.
2010-06-16 | E-GEOD-16567 | biostudies-arrayexpress
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.
2010-06-03 | GSE16567 | GEO
Project description:Since the roots of grapevine rootstocks have a direct contact with drying soil and has an important role in abiotic stimuli, any plasticity on the architecture of the rootstocks would enable grapevine varieties to a better respond to drought stress. However, genomics evidences behind the physiological responses of rootstocks under prolonged drought stress are poorly documented in the literature. In the current study, eight widely used hybrid grapevine rootstocks in viticulture were firstly grafted with sultana seedless and subjected to drought stress to test their physiological and biochemical responses. The results of experiment indicated that the roots of V.rupestris X V.berlandieri (110 R, 1103P, 140 Ru) rootstocks possessed much higher water content as well as non-structural carbohydrate and nitrogen concentrations compared to V.riparia X V.berlandieri (SO4, 5BB, 420A, 8B) and V.vinifera X V.berlandieri (41B) hybrids under drought. V.rupestris X V.berlandieri hybrids were also performed much higher root elongation performance under drought compared to other rootstock hybrids. Three rootstock varieties (110R, 5BB and 41B) having different pedigrees and root architectural responses to drought were also investigated at transcriptome level to find out gene regulation network behind differential physiological responses to drought. Transcriptome analysis revealed 2795, 1196 and 1612 differentially expressed transcripts for the roots of 110R, 5BB and 41B, respectively. The highest expression increases in 110R compared to other rootstocks were recorded for the transcripts functional in carbohydrate (SWEET14, CWINV) and nitrate/peptide (NRT1/ PTR FAMILY) transportation as well as osmoregulation (dehydrins, osmotins, LEAs and proline-glycine rich proteins) during drought. Higher induction of these genes in the roots of tolerant 110R genotype indicated importance of efficient uptake of carbohydrate and nitrogen source released from canopy under drought and preservation of water with osmotic regulation on the root elongation and drought tolerance of grapevines. Expression increases in several other pathogenesis related proteins, regulation of cell wall modification enzymes and activity of several secondary metabolites have been also associated to altered root architecture and drought tolerance in the grapevine rootstocks for the first time with the current study.
2016-10-25 | GSE89075 | GEO
Project description:Transcription factors play a crucial regulatory role in plant drought stress responses. In this study, a novel drought stress related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from transcriptome analysis of several typical rice varieties with different drought tolerance. The expression of OsbZIP62 was obviously induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while the osbzip62 mutants showed the opposite phenotype. RNA-seq analysis showed that many stress-related genes (e.g. OsGL1, OsNAC10, and DSM2) were up-regulated in OsbZIP62V plants. OsbZIP62 could bind to the abscisic acid–responsive element (ABRE) and promoters of several putative target genes. Taken together, OsbZIP62 positively regulated rice drought tolerance through regulated the expression of genes associated with stress.
2018-11-28 | GSE122887 | GEO
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding. To investigate the epigenetic effect on histone mark distribution of the EUE/PEG selection we performed ChIP-seq analyses. Native ChIP using an anti-H3K4me3 and no antibody (background control) was done on PEG1 and control plants.
2015-06-28 | E-GEOD-65571 | biostudies-arrayexpress