Clone-Dependent Expression of Esca Disease Revealed by Leaf Metabolite Analysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Moret F
PROVIDER: S-EPMC6333860 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Clone-Dependent Expression of Esca Disease Revealed by Leaf Metabolite Analysis.
Moret Florian F Lemaître-Guillier Christelle C Grosjean Claire C Clément Gilles G Coelho Christian C Negrel Jonathan J Jacquens Lucile L Morvan Guillaume G Mouille Grégory G Trouvelot Sophie S Fontaine Florence F Adrian Marielle M
Frontiers in plant science 20190109
Grapevine trutk diseases, especially Esca, are of major concern since they gradually alter vineyards worldwide and cause heavy economic losses. The expression of Esca disease symptoms depends on several factors, including the grapevine cultivar. In this context, a possible clone-dependent expression of the Esca disease was studied. Two clones of 'Chardonnay' grown in the same plot were compared according to their developmental and physiological traits, metabolome, and foliar symptom expression. ...[more]
Similar Datasets
Project description:Leaf samples were obtained from Vitis vinifera 'Malvasia Fina' plants with well-characterized esca complex disease symptoms (n = 18) and from healthy uninfected plants (n = 6). Leaves from diseased plants were divided into three groups: asymptomatic (ASY), chlorotic (SY1), and scorched leaves (SY2). The metabolic profile of these leaves was then examined using an ultrahigh performance liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization source. The number of small molecules measured in a sample was increased by varying the reconstitution solvent, chromatographic column, and ionization source. Data on accurate masses, peak areas, and relative levels of several metabolites were documented for each leaf sample, using the abovementioned approach. In this paper, data on 235 metabolites of known structural identity are reported, along with the biochemical pathways to which the metabolites belong. The remaining data related to lipid species and with a different focus of the research question are reported elsewhere. The broad coverage of metabolites reported here resulted in a greater coverage of the biochemical pathways involved in grapevine metabolism, which could provide a better understanding of the biochemical changes occurring during the onset and progression of foliar symptoms after invasion of woods by esca-associated pathogens. To determine which metabolites varied according to the study design, the detected ion features were processed using different statistical methods, including mean and median values, fold changes, Welch's two-sample t-test, false discovery rate, and quartiles represented by box and whisker plots. The goal of this statistical evaluation was to assess the responses of healthy, asymptomatic, and symptomatic leaf groups using a pairwise comparison, thus providing an opportunity for detecting statistically significant compounds and uncovering the dynamic metabolic models underlying disease latency and symptom expression.
| S-EPMC8627966 | biostudies-literature
Project description:Maize (Zea mays L.) is the most important food security crop worldwide. Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, severely reduces production causing millions of dollars in losses worldwide. Therefore, this study aimed to identify significant QTLs associated with NCLB by utilizing next-generation sequencing-based bulked-segregant analysis (BSA). Parental lines GML71 (resistant) and Gui A10341 (susceptible) were used to develop segregating population F2. Two bulks with 30 plants each were further selected from the segregating population for sequencing along with the parental lines. High throughput sequencing data was used for BSA. We identified 10 QTLs on Chr 1, Chr 2, Chr 3, and Chr 5 with 265 non-synonymous SNPs. Moreover, based on annotation information, we identified 27 candidate genes in the QTL regions. The candidate genes associated with disease resistance include AATP1, At4g24790, STICHEL-like 2, BI O 3-BIO1, ZAR1, SECA2, ABCG25, LECRK54, MKK7, MKK9, RLK902, and DEAD-box ATP-dependent RNA helicase. The annotation information suggested their involvement in disease resistance-related pathways, including protein phosphorylation, cytoplasmic vesicle, protein serine/threonine kinase activity, and ATP binding pathways. Our study provides a substantial addition to the available information regarding QTLs associated with NCLB, and further functional verification of identified candidate genes can broaden the scope of understanding the NCLB resistance mechanism in maize.
| S-EPMC9732028 | biostudies-literature
Project description:Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.
| S-EPMC9549252 | biostudies-literature
Project description:Studies on hepatitis C virus (HCV) replication have been greatly advanced by the development of cell culture models for HCV known as replicon systems. The prototype replicon consists of a subgenomic HCV RNA in which the HCV structural region is replaced by the neomycin phosphotransferase II (NPTII) gene, and translation of the HCV proteins NS3 to NS5 is directed by the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES). The interferon (IFN)-inducible protein kinase PKR plays an important role in cell defense against virus infection by impairing protein synthesis as a result of eIF-2alpha phosphorylation. Here, we show that expression of the viral nonstructural (NS) and PKR proteins and eIF-2alpha phosphorylation are all variably regulated in proliferating replicon Huh7 cells. In proliferating cells, induction of PKR protein by IFN-alpha is inversely proportional to viral RNA replication and NS protein expression, whereas eIF-2alpha phosphorylation is induced by IFN-alpha in proliferating but not in serum-starved replicon cells. The role of PKR and eIF-2alpha phosphorylation was further addressed in transient-expression assays in Huh7 cells. These experiments demonstrated that activation of PKR results in the inhibition of EMCV IRES-driven NS protein synthesis from the subgenomic viral clone through mechanisms that are independent of eIF-2alpha phosphorylation. Unlike NS proteins, HCV IRES-driven NPTII protein synthesis from the subgenomic clone was resistant to PKR activation. Interestingly, activation of PKR could induce HCV IRES-dependent mRNA translation from dicistronic constructs, but this stimulatory effect was mitigated by the presence of the viral 3' untranslated region. Thus, PKR may assume multiple roles in modulating HCV replication and protein synthesis, and tight control of PKR activity may play an important role in maintaining virus replication and allowing infection to evade the host's IFN system.
| S-EPMC136610 | biostudies-literature
Project description:We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabilities of 0.5-0.6. The average heritability of 0.25 was unaffected by the heading date. Correlations among metabolites reflected their functional grouping, highlighting the strict coordination of various routes of the citric acid cycle. Genome-wide association studies identified significant associations for six metabolic traits, namely oxalic acid, ornithine, L-arginine, pentose alcohol III, L-tyrosine, and a sugar oligomer (oligo II), with between one and 17 associated SNPs. Notable associations with genes regulating transcription or translation explained between 2.8% and 32.5% of the genotypic variance (pG). Further candidate genes comprised metabolite carriers (pG 32.5-38.1%), regulatory proteins (pG 0.3-11.1%), and metabolic enzymes (pG 2.5-32.5%). The combinatorial use of genomic and metabolic data to construct partially directed networks revealed causal inferences in the correlated metabolite traits and associated SNPs. The evaluated causal relationships will provide a basis for predicting the effects of genetic interferences on groups of correlated metabolic traits, and thus on specific metabolic phenotypes.
| S-EPMC5441906 | biostudies-literature
Project description:<p>Leaf samples were obtained from Vitis vinifera ‘Malvasia Fina’ plants with well-characterized esca complex disease symptoms (n = 18) and from healthy uninfected plants (n = 6). Leaves from diseased plants were divided into three groups: asymptomatic (ASY), chlorotic (SY1), and scorched leaves (SY2). The metabolic profile of these leaves was then examined using an ultrahigh performance liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization source. The number of small molecules measured in a sample was increased by varying the reconstitution solvent, chromatographic column, and ionization source. Data on accurate masses, peak areas, and relative levels of several metabolites were documented for each leaf sample, using the abovementioned approach. In this paper, data on 235 metabolites of known structural identity are reported, along with the biochemical pathways to which the metabolites belong. The remaining data related to lipid species and with a different focus of the research question are reported elsewhere. The broad coverage of metabolites reported here resulted in a greater coverage of the biochemical pathways involved in grapevine metabolism, which could provide a better understanding of the biochemical changes occurring during the onset and progression of foliar symptoms after invasion of woods by esca-associated pathogens. To determine which metabolites varied according to the study design, the detected ion features were processed using different statistical methods, including mean and median values, fold changes, Welch's two-sample t-test, false discovery rate, and quartiles represented by box and whisker plots. The goal of this statistical evaluation was to assess the responses of healthy, asymptomatic, and symptomatic leaf groups using a pairwise comparison, thus providing an opportunity for detecting statistically significant compounds and uncovering the dynamic metabolic models underlying disease latency and symptom expression.</p>
2021-11-21 | MTBLS353 | MetaboLights
Project description:Esca of grapevine causes yield losses correlated with incidence and severity symptom expression. Factors associated with leaf symptom mechanisms are yet to be fully clarified. Therefore, in 2019 and 2020, macro and microelement analyses and leaf reflectance measurements were carried out on leaves at different growth stages in a vineyard located in Abruzzo, central Italy. Surveys were carried out on leaves of both never leaf-symptomatic vines and different categories of diseased vine shoots. Never leaf-symptomatic and diseased vines were also treated with a fertilizer mixture that proved to be able to limit the symptom expression. Results showed that untreated asymptomatic diseased vines had high calcium contents for most of the vegetative season. On the contrary, treated asymptomatic diseased vines showed higher contents of calcium, magnesium, and sodium, at berries pea-sized, before the onset of symptoms. These vines had better physiological efficiency showing higher water index (WI), normalized difference vegetation index (NDVI), and green normalized difference vegetation index (GNDVI) values, compared to untreated asymptomatic vines, at fruit set. Results confirmed the strong response of the plant to symptom expression development and the possibility of limiting this response with calcium and magnesium applications carried out before the symptom onset.
| S-EPMC8224345 | biostudies-literature
Project description:BackgroundBetter understanding of the physiological and metabolic status of plants can only be obtained when metabolic fluxes are accurately assessed in a growing plant. Steady state 13C-MFA has been established as a routine method for analysis of fluxes in plant primary metabolism. However, the experimental system needs to be improved for continuous carbon enrichment from labelled sugars into metabolites for longer periods until complex secondary metabolism reaches steady state.ResultsWe developed an in vitro plant culture strategy by using peppermint as a model plant with minimizing unlabelled carbon fixation where growing shoot tip was strongly dependent on labelled glucose for their carbon necessity. We optimized the light condition and detected the satisfactory phenotypical growth under the lower light intensity. Total volatile terpenes were also highest at the same light. Analysis of label incorporation into pulegone monoterpene after continuous U-13C6 glucose feeding revealed nearly 100% 13C, even at 15 days after first leaf visibility (DALV). Label enrichment was gradually scrambled with increasing light intensity and leaf age. This study was validated by showing similar levels of label enrichment in proteinogenic amino acids. The efficiency of this method was also verified in oregano.ConclusionsOur shoot tip culture depicted a method in achieving long term, stable and a high percentage of label accumulation in secondary metabolites within a fully functional growing plant system. It recommends the potential application for the investigations of various facets of plant metabolism by steady state 13C-MFA. The system also provides a greater potential to study sink leaf metabolism. Overall, we propose a system to accurately describe complex metabolic phenotypes in a growing plant.
| S-EPMC6526604 | biostudies-literature
Project description:Within-canopy variation in leaf structural and photosynthetic characteristics is a major means by which whole canopy photosynthesis is maximized at given total canopy nitrogen. As key acclimatory modifications, leaf nitrogen content (N A) and photosynthetic capacity (A A) per unit area increase with increasing light availability in the canopy and these increases are associated with increases in leaf dry mass per unit area (M A) and/or nitrogen content per dry mass and/or allocation. However, leaf functional characteristics change with increasing leaf age during leaf development and aging, but the importance of these alterations for within-canopy trait gradients is unknown. I conducted a meta-analysis based on 71 canopies that were sampled at different time periods or, in evergreens, included measurements for different-aged leaves to understand how within-canopy variations in leaf traits (trait plasticity) depend on leaf age. The analysis demonstrated that in evergreen woody species, M A and N A plasticity decreased with increasing leaf age, but the change in A A plasticity was less suggesting a certain re-acclimation of A A to altered light. In deciduous woody species, M A and N A gradients in flush-type species increased during leaf development and were almost invariable through the rest of the season, while in continuously leaf-forming species, the trait gradients increased constantly with increasing leaf age. In forbs, N A plasticity increased, while in grasses, N A plasticity decreased with increasing leaf age, reflecting life form differences in age-dependent changes in light availability and in nitrogen resorption for growth of generative organs. Although more work is needed to improve the coverage of age-dependent plasticity changes in some plant life forms, I argue that the age-dependent variation in trait plasticity uncovered in this study is large enough to warrant incorporation in simulations of canopy photosynthesis through the growing period.
| S-EPMC5818143 | biostudies-other
Project description:The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46,093 soybean genes, which were predicted with high confidence among approximately 66,000 putative genes, 41,059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of many photosynthesis-related genes, which contribute to growth retardation under drought stress, may serve as an adaptive mechanism for plant survival. This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.
| S-EPMC3505142 | biostudies-literature