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Unravelling the transcriptome and metabolite modulation of superficial scald development in pear fruit (cv. ‘Blanquilla’)

ABSTRACT: Unravelling the transcriptome and metabolite modulation of superficial scald development in pear fruit (cv. ‘Blanquilla’)

PROVIDER: PRJNA562311 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10045100.fastq.gz	Fastqsanger.gz
	SRR10045101.fastq.gz	Fastqsanger.gz
	SRR10045102.fastq.gz	Fastqsanger.gz
	SRR10045094.fastq.gz	Fastqsanger.gz
	SRR10045095.fastq.gz	Fastqsanger.gz

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Similar Datasets

Unravelling the transcriptome and metabolite modulation of superficial scald development in pear fruit (cv. ‘Blanquilla’)

Project description:The harveting of the fruit of a single cultivar are technically harvested over a period of time and the progression of the on-tree fruit maturity lead to important physiological modification and transcriptional signature able to impact the final quality of fruit and the management of the postharvest phase.

2020-04-10 | GSE136374 | GEO

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

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

Investigation of the transcriptomic and metabolic changes associated with superficial scald physiology impaired by lovastatin and 1-methylcyclopropene in pear fruit (cv. "Blanquilla").

Project description:To elucidate the physiology underlying the development of superficial scald in pears, susceptible "Blanquilla" fruit was treated with different compounds that either promoted (ethylene) or repressed (1-methylcyclopropene and lovastatin) the incidence of this disorder after 4 months of cold storage. Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin, but highly manifested in untreated (78% incidence) or ethylene-treated fruit (97% incidence). The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment. In all treated samples, cold storage led to an activation of a cold-acclimation-resistance mechanism, including the biosynthesis of very-long-chain fatty acids, which was especially evident in 1-methylcyclopropane-treated fruit. Among the treatments applied, only 1-methylcyclopropene inhibited ethylene production, hence supporting the involvement of this hormone in the development of scald. However, a common repression effect on the PPO gene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples, suggesting also a non-ethylene-mediated process preventing the development of this disorder. The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.

| S-EPMC7109095 | biostudies-literature

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

Transcriptomic Insights on the Preventive Action of Apple (cv Granny Smith) Skin Wounding on Superficial Scald Development.

Project description:Superficial scald is a post-harvest chilling storage injury leading to browning of the surface of the susceptible cv Granny Smith apples. Wounding of skins has been reported to play a preventive role on scald development however its underlying molecular factors are unknown. We have artificially wounded the epidermal and sub-epidermal layers of apple skins consistently obtaining the prevention of superficial scald in the surroundings of the wounds during two independent vintages. Time course RNA-Seq analyses of the transcriptional changes in wounded versus unwounded skins revealed that two transcriptional waves occurred. An early wave included genes up-regulated by wounding already after 6 h, highlighting a specific transcriptional rearrangement of genes connected to the biosynthesis and signalling of JA, ethylene and ABA. A later transcriptional wave, occurring after three months of cold storage, included genes up-regulated exclusively in unwounded skins and was prevented from its occurrence in wounded skins. A significant portion of these genes was related to decay of tissues and to the senescence hormones ABA, JA and ethylene. Such changes suggest a wound-inducible reversed hormonal balance during post-harvest storage which may explain the local inhibition of scald in wounded tissues, an aspect that will need further studies for its mechanistic explanation.

| S-EPMC8705499 | biostudies-literature

Comparative Transcriptome Analysis Reveals Insight into Exocarp Russeting Pear Variety

Project description:We carried out the transcriptome analysis to identify the key genes involved in pear fruit russet formation by comparing five pear varieties with distinct exocarp characteristics

2023-06-30 | GSE193982 | 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

RNA-Seq Data from fruit skin of sand pear

Project description:Transcriptom data of pear fruit skin

2019-11-05 | GSE139895 | 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

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