Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative transcriptome and metabolomic survey reveal key pathways involved in the control of the chilling injury disorder superficial scald in two apple cultivars, ‘Granny Smith’ and ‘Ladina’

ABSTRACT: Comparative transcriptome and metabolomic survey reveal key pathways involved in the control of the chilling injury disorder superficial scald in two apple cultivars, ‘Granny Smith’ and ‘Ladina’

PROVIDER: PRJNA892066 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21971335.fastq.gz	Fastqsanger.gz
	SRR21971336.fastq.gz	Fastqsanger.gz
	SRR21971337.fastq.gz	Fastqsanger.gz
	SRR21971338.fastq.gz	Fastqsanger.gz
	SRR21971339.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Comparative transcriptome and metabolomic survey reveal key pathways involved in the control of the chilling injury disorder superficial scald in two apple cultivars, ‘Granny Smith’ and ‘Ladina’

Project description:The low temperature normally applied to prevent fruit decay during the storage of apples, can also triggers the onset of a chilling injury disorder known as superficial scald. In this work, the etiology of this disorder and the mechanism of action of two preventing strategies, such as the application of 1-MCP and storage at low oxygen concentration in ‘Granny Smith’ and ‘Ladina’ apple cultivars was investigated. The metabolite assessment highlighted a reorganization of specific secondary metabolites, in particular flavan-3-ols (catechin, epicatechin and procyanidin B) and unsaturated fatty acids (oleic acid, linoleic acid and linolenic acid), while the genome-wide transcriptomic analysis grouped the DEGs into four functional clusters. The KEGG pathway, GO enrichment analysis, together with the gene-metabolite profiling interactome, showed as the treatment with 1-MCP prevented the development of superficial scald by actively promoting the production of unsaturated fatty acids, especially in ‘Granny Smith’. ‘Ladina’ was instead more susceptible to superficial scald, and characterized by a higher accumulation of very long chain fatty acids (VLCFAs). Storage at low oxygen concentration stimulated a higher accumulation of ethanol and acetaldehyde together with the expression of genes involved in anaerobic respiration, such as malate and alcohol dehydrogenase and pyruvate decarboxylase in both cultivars. Moreover, in ‘Granny Smith’ apple, the expression of three members of the VII subgroups of ERF genes, encoding for elements coordinating the acclimation process to hypoxia in plants was observed. The global RNA-Seq pattern also elucidated a specific transcriptomic signature between the two cultivars, validating the effect of the different genetic background in the control of this disorder.

2023-03-29 | GSE216082 | GEO

Transcriptional profiling of Granny Smith apple peel (Malus x domestica Borkh) at harvest between contrasted years for scald incidence

Project description:Granny Smith apples (Malus x domestica Borkh) were harvested at early physiological mature stage in 2014, 2015 and 2017 and phenotyped for scald incidence after long time cold storage. Differential analyses were set-up for peel samples collected at harvest between fruit batches with low or high scald incidence.

2020-04-20 | GSE135863 | GEO

Transcriptome and metabolic survey disclose the mode of action of static and dynamic low oxygen postharvest storage strategies to prevent the onset of superficial scald disorder in fruit of ‘Granny Smith’ apple cultivar

Project description:To preserve quality feature and ensuring availability of fresh fruit on the market, apples need to be stored. The low temperature applied during storage, beside avoiding important fruit loss, can also promote the development of serious chilling injury type of disorder, such as superficial scald. One of the strategies largely employed to prevent the development of this phenomenon is the control of the storage atmosphere, by lowering down the concentration of oxygen. In this work, a multifaceted survey was carried out to investigate the variation in transcriptome together with three categories of metabolites (phenolics, lipids and volatile organic compounds, VOCs) in fruit of ‘Granny Smith’ apple cultivar stored in both static and dynamic hypoxia condition for 5 and 7 months, respectively. The global transcriptome survey identified a core set of differentially expressed genes in three main functional groups, revealing as the duration of storage had an important effect in the coordination of gene expression. The effect of the storage time was furthermore highlighted by the DEG-network analysis that identified a distinct number and type of transcriptomic hubs. Samples characterized by the development of superficial scald were distinguished by a higher concentration of chlorogenic acid and a higher expression of PAL and PPO in a time specific fashion. The prevention of this phenomenon was instead related to distinctive re-programming events, involving the accumulation of specific antioxidant types of metabolites, very long chain fatty acids and the expression of genes coordinating an hypoxia acclimation process, such as RAP2-like and PCO.

2023-12-31 | GSE225233 | GEO

Effect of 1-methylcyclopropene (1-MCP) and ozone (Ο 3 ) post-harvest treatments on the proteomic profiling of Granny Smith apple peel (Malus x domestica Borkh) after cold storage

Project description:Superficial scald is a major physiological disorder in apple fruit that is induced by cold storage and is mainly expressed as brown necrotic patches on peel tissue. However, a global view of the gene-protein-metabolite interactome underlying scald prevention/sensitivity is currently missing. Herein, we have found for the first time that cold storage in an atmosphere enriched with ozone (O3) induced scald symptoms in ‘Granny Smith’ apple fruits during subsequent ripening at room temperature. In contrast, treatment with the ethylene perception inhibitor 1-methylcyclopropene (1-MCP) reversed this O3-induced scald effect. Amino acids, including branched-chain amino acids, were the most strongly induced metabolites in peel tissue of 1-MCP treated fruits. Proteins involved in oxidative stress and protein trafficking were differentially accumulated prior to and during scald development. Genes involved in photosynthesis, flavonoid biosynthesis and ethylene signaling displayed significant alterations in response to 1-MCP and O3. Analysis of regulatory module networks identified putative transcription factors (TFs) that could be involved in scald. Subsequently, a transcriptional network of the genes-proteins-metabolites and the connected TFs was constructed. This approach enabled identification of several genes co-regulated by TFs, notably encoding glutathione S-transferase (GST) protein(s) with distinct signatures following 1-MCP and O3 treatments. Overall, this study is an important contribution to future functional studies and breeding programs for this fruit, aiding to the development of improved apple cultivars to superficial scald.

2020-05-27 | PXD016849 | Pride

Malus domestica breed:Granny smith

Project description:Malus domestica breed:Granny smith Genome sequencing

| PRJNA1168436 | ENA

Malus domestica cultivar:Granny smith

Project description:Malus domestica cultivar:Granny smith Genome sequencing

| PRJNA1168439 | ENA

Malus domestica cultivar:Granny Smith

Project description:Malus domestica cultivar:Granny Smith Raw sequence reads

| PRJNA803936 | ENA

Ethylene -dependent and -independent superficial scald resistance mechanisms in 'Granny Smith' apple fruit.

Project description:Superficial scald is a major physiological disorder of apple fruit (Malus domestica Borkh.) characterized by skin browning following cold storage; however, knowledge regarding the downstream processes that modulate scald phenomenon is unclear. To gain insight into the mechanisms underlying scald resistance, 'Granny Smith' apples after harvest were treated with diphenylamine (DPA) or 1-methylcyclopropene (1-MCP), then cold stored (0 °C for 3 months) and subsequently were ripened at room temperature (20 °C for 8 days). Phenotypic and physiological data indicated that both chemical treatments induced scald resistance while 1-MCP inhibited the ethylene-dependent ripening. A combination of multi-omic analysis in apple skin tissue enabled characterization of potential genes, proteins and metabolites that were regulated by DPA and 1-MCP at pro-symptomatic and scald-symptomatic period. Specifically, we characterized strata of scald resistance responses, among which we focus on selected pathways including dehydroabietic acid biosynthesis and UDP-D-glucose regulation. Through this approach, we revealed scald-associated transcriptional, proteomic and metabolic signatures and identified pathways modulated by the common or distinct functions of DPA and 1-MCP. Also, evidence is presented supporting that cytosine methylation-based epigenetic regulation is involved in scald resistance. Results allow a greater comprehension of the ethylene-dependent and -independent metabolic events controlling scald resistance.

| S-EPMC6065312 | biostudies-literature

Apple fruit superficial scald resistance mediated by ethylene inhibition is associated with diverse metabolic processes

Project description:Fruits stored at low temperature for long time can undergo to different type of chilling injuries. In apple, superficial scald represents one of the most serious physiopathy. The typical symptoms of this disorder are represented by the development of important discoloration and black patches on the fruit exocarp. Although this phenomenon has been historically related to α-farnesene, its etiology and physiology are not yet fully disclosed. In the attempt to elucidate the regulating mechanism of its development and prevention, a multidisciplinary survey was performed, integrating different level of metabolite screening (volatiles, polyphenols and lipids) with a large-scale transcriptomic analysis. The comparison between scalded and non-scalded apples (treated with an ethylene competitor) revealed that the prevention of superficial scald is associated with the triggering of cold acclimation-related processes. The interference at the ethylene receptor level stimulates the production of antioxidant compounds to scavenge reactive oxygen species (ROS), the synthesis of unsaturated fatty acids to stabilize plastid and vacuole membranes against cold temperature and the accumulation of sugar alcohols with important cryoprotectant roles, such as sorbitol. The accumulation pattern of this polyalcohol was also consistent with the expression profile of MdS6PDH. Moreover, the overexpression of this gene in transgenic line of Arabidopsis thaliana plants provided functional validation of its involvement in the biosynthetic pathway of sorbitol and elucidated its role in the cold acclimation and freezing tolerance process.

2019-05-02 | GSE98893 | GEO

Transcriptomic and GC-MS metabolomic analysis to provide insight into aroma volatile compounds of ‘Granny Smith’ and ‘Jonagold’ apples (Malus domestica)

Project description:In order to know more about the expression levels of aroma-related genes involved in the metabolic pathways, transcriptome sequencing of Granny Smith and Jonagold apples was conducted utilizing the Illumina platform. Our study provides new insights on the understanding of transcriptional regulatory mechanisms associated with aroma volatiles formation in apples.

2022-03-02 | GSE176136 | 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