Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ecophysiological and molecular basis of drought responses in forest trees: the modulating role of canopy structure and light environment

ABSTRACT: Climate change forecasts increase the susceptibility of forest due to longer drier seasons. The adaptive management protocols have highlighted the reduction of the forest densification to improve their vulnerability to extreme climate events (i.g. drought). One of this sensitive woody species to climate change is the Abies pinsapo, a relic conifer tree endemic from the southern Spain. Previous works have shown changes in their trends because of the climate change action, being carried out experimental thinning management in their lowest distribution limit, in Sierra de las Nieves Natural Park (Malaga). Our objective is to evaluate the water improvements of thinned trees in terms of light availability by means of a shading treatment in those thinned trees. To do that we have evaluated the synergic effect of ecophysiology, metabolomics and transcriptomics in control, thinning and thinning+shading plots in wet and dry seasons for two years. The results showed strong differences between summer and spring seasons at the three studied levels. The water deficit shows a greater influence than light exposure in the ecophysiology and metabolomics tree response. And the transcriptomics suggested an improvement of thinned trees when light exposure was reduced. Our results support the necessity of adaptive forest management in order to improve the conservation status of A. pinsapo forest. The combination of different levels of tree response is paramount to understand and predict the tree physiology under water and light stress conditions.

ORGANISM(S): Abies pinsapo

PROVIDER: GSE208073 | GEO | 2022/07/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of mycorrhized European beech (Fagus sylvatica L.) roots in response to fertilization with different forms of inorganic nitrogen

Project description:Young Fagus sylvatica trees (approximately 7 to 8 years) were collected from a natural regeneration beech forest. The trees were excavated with intact soil cores, roots and top organic layer. The trees were then kept outdoors at the Department of Forest Botany, Georg-August-Universität Göttingen. Plants were protected from rain, and light conditions were matched to those of the natural stand using a shading net; otherwise, plants were exposed to natural climatic conditions. The soil moisture was regularly measured; plants were watered with deionized water as needed to keep soil moisture close to the original conditions. Trees was randomly relocated on a weekly basis throughout the experiment to avoid biasses caused by location or light effects. After 21 weeks, a treatment was applied to understand the physiological mechanisms of inorganic nitrogen uptake and assimilation under conditions of an inorganic nitrogen saturated forest simulation: Plants were fertilized with either a 20 mM solution of KNO3, a 20 mM solution of NH4Cl, or demineralized water (control) for 2 days. On the third day, the trees were harvested. Root tips were immediately shock-frozen in liquid nitrogen and used for RNA extraction.

2020-12-14 | E-MTAB-8931 | biostudies-arrayexpress

Proteome data on soil microbial community

Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.

2021-02-02 | PXD005447 | Pride

Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

Project description:Background: Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning. Results: We profiled the transcriptome of Vitis vinifera cv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m2 leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed. Conclusion: Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process. Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three cluster thinned vines (50% of cluster removed) at beginning of véraison (BV), end of véraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.

2012-03-05 | E-GEOD-36234 | biostudies-arrayexpress

Abiotic stress response and adaptive phenology in fruit trees

Project description:Due to the broad climate adaptation of perennial trees, phenological traits (e.g. chilling requirement-CR, bloom date-BD) exhibit complex inheritance patterns. Conceptually, these are adaptive responses to abiotic stress. As production depends on traits like CR, breeders have developed varieties that are phenotypically/genotypically matched to particular geographic/temperature zones. These genotypes are ideal for study of gene networks governing these climate-critical traits. Using genetic approaches, genome-wide association analyses, functional and comparative genomics in fruit and forest trees, we identified a foundational network of genetic activity (phenylpropanoid pathway) linking winter cold stress response to control of the endodormancy-ecodormancy transition (EET) and seed stratification. Our goal is to examine during endodormancy the allelic effects of genes controlling the production of stress related metabolic intermediates that regulate seed stratification, thus linking these two cold temperature responses. Our objective is to use a transcriptome sequencing approach to characterize genotypic effects on the phenylpropanoid gene network transcriptome during endodormancy and the EET. These adaptive genes and gene networks will be targets for knowledge based breeding strategies of fruit and forest trees to sustain and improve these resources to meet the challenges of rapid environmental change

2020-03-23 | GSE138792 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in leaves of two subtropical trees grown under contrasting light

Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.

2018-10-01 | GSE104004 | GEO

Study of poplar shoot apex methylome response to variations in soil water avaialbility

Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, DNA methylation patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Transcriptomic response was also studied and is another GEO submission.

2014-01-01 | GSE46624 | GEO

Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

2012-03-05 | GSE36234 | GEO

Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response_DataSet1

Project description:We investigated the transcriptional response of hybrid poplar (Populus trichocarpa x deltoides) leaves to a variety of stress treatments (insect feeding by Malacosoma disstria larvae, mechanical wounding, and wounding plus the application of insect oral secretions) over a 24 hour time course. Experiments were conducted using clonal trees under greenhouse conditions at the University of British Columbia. We used the 15.5K poplar cDNA microarray platform previously described by Ralph et al. (Molecular Ecology 2006, 15:1275-1297). Differentially expressed genes were determined using three criteria: fold-change between treated and untreated control leaves > 1.5-fold, P value < 0.05 and Q value < 0.05. This study identified > 1,000 differentially expressed genes in response to insect feeding and/or treatments that mimic insect feeding damage. A factorial hybridization design was chosen to assess gene expression among the untreated control leaves, and leaves subjected to one of three stress treatments: forest tent caterpillar (Malacosoma disstria) feeding, mechanical wounding, and mechanical wounding plus the application of forest tent caterpillar oral secretions. For each tree, the lowest five mature leaves were caged in nylon mesh bags, treated or left untreated as a control. Leaves were harvested 2, 6 or 24 hours after the initiation of each treatment and total RNA was individually isolated from each tree. For each treatment and time point, equal amounts of total RNA were combined from each of the five biological replicate trees prior to cDNA microarray analysis. For the herbivory, mechanical wounding and oral secrection treatments, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations.

2008-12-30 | E-GEOD-13767 | biostudies-arrayexpress

Identification of candidate genes affecting juvenile wood stiffness in Pinus radiata

Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared.

2011-06-01 | GSE23020 | GEO

Study of poplar shoot apex transcriptomic response to variations in soil water avaialbility

Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found.

2014-01-01 | GSE46605 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data