Reverse genomic analysis of ethylene signaling in apple fruit
Ontology highlight
ABSTRACT:
ORGANISM(S): Malus domestica
PROVIDER: GSE17678 | GEO | 2018/03/01
REPOSITORIES: GEO
Similar Datasets
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:The ripening of climacteric fruits, such as apple, is represented by a series of genetically programmed events orchestrated by the action of several hormones. In this work, we investigated the existence of a hormonal crosstalk between ethylene and auxin during the post-harvest ripening of three internationally known apple cultivars: ‘Golden Deli-cious’, ‘Granny Smith’ and ‘Fuji’. The normal climacteric ripening was impaired by the exogenous application of 1-methylcyclopropene (1-MCP) that effectively affected the production of ethylene and the physiological behaviour of specific ethylene-related qual-ity traits, such as fruit texture and the production of volatile organic compounds showed a de-novo accumulation of auxin following the application of 1-MCP. The RNA-Seq wide-transcriptome analysis evidenced as the competition at the level of the ethylene re-ceptors induced a cultivar-dependent transcription re-programming. The DEGs annota-tion carried out through the KEGG database identified as most genes were assigned to the plant hormone signaling transduction category, and specifically related to auxin and ethylene. The interplay between these two hormones was further assessed through a candidate gene analysis that highlighted a specific activation of GH3 and ILL genes, en-coding key steps in the process of the auxin homeostasis mechanism. Our results showed that a compromised ethylene metabolism at the onset of the climacteric ripening in apple can stimulate, in a cultivar-dependent fashion, an initial de-novo synthesis and de-conjugation of auxin as a tentative to restore a normal ripening progression.
2021-11-17 | GSE182822 | 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 | 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: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
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.
2010-11-05 | GSE24523 | GEO
Project description:The ethylene-auxin crosstalk regulates the postharvest fruit ripening process in apple
| PRJNA758010 | 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. 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:Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.
2018-07-04 | GSE116581 | GEO
Project description:Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes in order to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, ELISA-based glycomics profiling of fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectin polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbcpg1Δbcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
2022-01-01 | GSE183836 | GEO