Malus domestica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA720061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14241306_1.fastq.gz | Fastqsanger.gz | |||
| SRR14241306_2.fastq.gz | Fastqsanger.gz | |||
| SRR14241307_1.fastq.gz | Fastqsanger.gz | |||
| SRR14241307_2.fastq.gz | Fastqsanger.gz | |||
| SRR14241308_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Transcriptome sequencing project for related process of ripening apple fruit
| PRJNA725798 | ENA
Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation. 48 samples analyzed; 8 stages have been identified over the fruit development and ripening (from flower to post harvest ripening) of apple fruit belonging to two apple cultivars (Golden Delicious and Granny Smith), ending with 16 samples (3 replacates for each sample)
2016-08-23 | E-GEOD-78745 | biostudies-arrayexpress
Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation. whole genome array specifically enriched of ripening related genes for apple (WGAA) with two cultivars (Golden Delicious and Granny Smith)
2016-08-23 | E-GEOD-78744 | biostudies-arrayexpress
Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation.
2016-08-23 | GSE78745 | GEO
Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation.
2016-08-23 | GSE78744 | GEO
Project description:Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes
| PRJNA132655 | ENA
Project description:Apple is typically stored under low temperature and controlled atmospheric conditions to ensure a year round supply of high quality fruit for the consumer. During storage, losses in quality and quantity occur due to spoilage by postharvest pathogens. One important postharvest pathogen of apple is Botrytis cinerea. The fungus is a broad host necrotroph with a large arsenal of infection strategies able to infect over 1,400 different plant species. We studied the apple-B. cinerea interaction to get a better understanding of the defense response in apple. We conducted an RNAseq experiment in which the transcriptome of inoculated and non-inoculated (control and mock) apples was analyzed at 0, 1, 12 and 28 h post inoculation. Our results show extensive reprogramming of the apple's transcriptome with about 28.9 % of expressed genes exhibiting significant differential regulation in the inoculated samples. We demonstrate the transcriptional activation of pathogen-triggered immunity and a reprogramming of the fruit’s metabolism. We demonstrate a clear transcriptional activation of secondary metabolism and a correlation between the early transcriptional activation of the mevalonate pathway and reduced susceptibility, expressed as a reduction in resulting lesion diameters. This pathway produces the building blocks for terpenoids, a large class of compounds with diverging functions including defense. 1-MCP and hot water dip treatment are used to further evidence the key role of terpenoids in the defense and demonstrate that ethylene modulates this response.
2022-03-01 | GSE195841 | GEO
Project description:Apple (Malus domestica Borkh) is an important fruit crop cultivated in a broad range of environmental conditions. Apple fruit, and specifically peel tissue, ripening is a physiological process whose molecular regulatory networks response to different environments are still not sufficiently investigated. In this study, the influence of low (20 m) and high (750 m) altitude environmental conditions in peel tissue was assessed by physiological measurements combined with global metabolite and protein expression profiling during apple fruit development and ripening. Although apple fruit ripening was unaffected by the different environmental conditions, however several key color parameters, such as redness and the color percentage index, were induced by high altitude. Consistent with this, increased level of anthocyanin and other phenolic compounds, including cyanidin-3-O-galactoside, quercetin-3-O-rhamnoside, quercetin-3-O-rutinoside and chlorogenic acid were identified in apple peel at high altitude. Also, high altitude environment, particularly, at the ripening period, up-accumulated various carbohydrates (eg., arabinose, xylose and sucrose) while repressed glutamic acid and several related proteins such as glycine hydroxymethyltransferase and glutamate–glyoxylate aminotransferase. Other processes affected by high altitude concerned the TCA cycle, the synthesis of oxidative/defense enzymes, and the accumulation of photosynthetic proteins. Finally, we constructed a metabolite-protein network depicting the impact of altitude on peel ripening. These data provide insights into physiological processes linked to apple peel ripening across different climatic conditions and will assist in efforts to improve apple fruit appeal and quality.
2021-09-08 | PXD017037 | Pride
Project description:Apple (Malus domestica Borkh) is an important fruit crop cultivated in a broad range of environmental conditions. Apple fruit, and specifically peel tissue, ripening is a physiological process whose molecular regulatory networks response to different environments are still not sufficiently investigated. In this study, the influence of low (20 m) and high (750 m) altitude environmental conditions in peel tissue was assessed by physiological measurements combined with global metabolite and protein expression profiling during apple fruit development and ripening. Although apple fruit ripening was unaffected by the different environmental conditions, however several key color parameters, such as redness and the color percentage index, were induced by high altitude. Consistent with this, increased level of anthocyanin and other phenolic compounds, including cyanidin-3-O-galactoside, quercetin-3-O-rhamnoside, quercetin-3-O-rutinoside and chlorogenic acid were identified in apple peel at high altitude. Also, high altitude environment, particularly, at the ripening period, up-accumulated various carbohydrates (eg., arabinose, xylose and sucrose) while repressed glutamic acid and several related proteins such as glycine hydroxymethyltransferase and glutamate���glyoxylate aminotransferase. Other processes affected by high altitude concerned the TCA cycle, the synthesis of oxidative/defense enzymes, and the accumulation of photosynthetic proteins. Finally, we constructed a metabolite-protein network depicting the impact of altitude on peel ripening. These data provide insights into physiological processes linked to apple peel ripening across different climatic conditions and will assist in efforts to improve apple fruit appeal and quality.
2021-11-25 | PXD017057 | Pride
Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes. Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.
2010-11-05 | E-GEOD-24523 | biostudies-arrayexpress