RNA-seq of fruit of pear with a different on-tree maturity
Ontology highlight
ABSTRACT:
ORGANISM(S): Pyrus communis
PROVIDER: GSE113517 | GEO | 2019/03/18
REPOSITORIES: GEO
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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
Project description:RNA-seq of fruit of pear with a different on-tree maturity
| PRJNA451427 | ENA
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:Table grapes cv. Cardinal are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment with 20 kPa CO2 at 0C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes. Table grapes harvested at two maturity stages (early and late). 3 biological replicates. Early-harvested (MI:12.45) : Time zero, 3 days air 0C, 3 days high CO2 levels 0C. Late-harvested (MI: 41.08): Time zero, 3 days air 0C, 3 days high CO2 levels 0C.
2016-09-04 | E-GEOD-83275 | biostudies-arrayexpress
Project description:Fig fruit are highly perishable at the tree-ripe (TR) stage. Commercial-ripe (CR) fruit, which are harvested before the TR stage for their postharvest transportability and shelf-life advantage, are inferior to TR fruit in size, color and sugar content. The succulent urn-shaped receptacle serves as the protective structure and edible part of the fruit, and determines fruit quality. Quantitative iTRAQ reveal the proteins and transcripts that are differentially expressed in fig receptacle at the two harvest stages. We annotated 691 proteins against uni_Moraceae_3487, of which 59 showed ≤1.3 -fold change—in TR vs CR fruit. Ficin was the most abundant soluble protein in the fig receptacle. A high abundance of aminocyclopropane-1-carboxylate oxidase was identified.
2019-03-22 | PXD009757 | Pride
Project description:A custom oligoarray of Japanese pear (Pyrus pyrifolia) based on 9,812 independent ESTs from different tissues (fruits at various growth stages, vegetative and flower tissues) was designed and used for comprehensive investigation of gene expression before and during ripening (105 to 147 days after full bloom). Gene expression in fruit development of Japanese pear was measured from 105 to 147 days after full bloom (DAFB). 147 DAFB is the optimum maturity for eating. Two to three independent experiments were performed at each time (105 to 147 DAFB) using different trees for each experiment.
2010-10-12 | E-GEOD-18682 | biostudies-arrayexpress
Project description:Background: Anthocyanins are the most important compounds for nutritional quality and economic values of blood orange. However, there are few reports on the pre-harvest treatment accelerate the accumulation of anthocyanins in postharvest blood orange fruit. Here, we performed a comparative Transcriptome and metabolomics analysis to elucidate the underlying mechanism involved in seasonal drought (SD) treatment during fruit expansion stage on anthocyanin accumulation in postharvest ‘Tarocco’ blood orange fruit. Results: Our results showed that SD treatment slowed down the fruit enlargement and increased the sugar accumulation during fruit development and matured period. Obviously, under SD treatment, the accumulation of anthocyanin in blood orange fruit during postharvest storage was significantly accelerated and markedly higher than that in CK. Meanwhile, the total flavonoids and phenols contents and antioxidant activity in SD treatment fruit were also sensibly increased during postharvest storage. Based on metabolome, we found that substrates required for anthocyanin biosynthesis, such as amino acids and their derivatives, and phenolic acids, have significantly accumulated and higher in SD treated mature fruit compared with that of CK. Further according to the results of transcriptome data and weighted gene coexpression correlation network analysis (WGCNA) analysis, phenylalanine ammonia-lyase (PAL3) was considered key structural gene. qRT-PCR analysis verified that the PAL3 was highly expressed in SD treated postharvest stored fruit and was significantly positively correlated with the anthocyanin content. Moreover, we found that other structural genes in anthocyanin biosynthesis pathway were also upregulated under SD treatment through transcriptome data and qRT-PCR analysis. Conclusions: The findings suggest that SD treatment promotes the accumulation of substrates necessary for anthocyanin biosynthesis during fruit ripening process, and activates the expression of anthocyanin biosynthesis pathway genes during postharvest storage period, especially PAL3, co-contributed to the rapid accumulation of anthocyanin. The present study provides a theoretical basis for postharvest quality control and water-saving utilization of blood orange fruit.
2024-03-06 | GSE253283 | GEO
Project description:Gene expression associated with apple fruit ripening and postharvest treatments was studied to identify transcripts that are regulated by ethylene signaling.
2018-03-01 | GSE17678 | GEO
Project description:Five rootstock cultivars of differing vigor: vigorous (Atlas and Brights Hybrid 5), standard (Krymsk 86 and Lovell) and dwarfing (Krymsk 1) with Redhaven as scion were studied for their impact on internal fruit quality and maturity. Five years of data showed that average yield (kg per tree) and fruit count increased significantly with increasing vigor (trunk cross sectional area, TCSA), however, no difference was observed in fruit size across rootstocks. In 2019, a detailed peach fruit quality analysis on fruit of equal maturity (based on index of absorbance difference, IAD) coming from trees with equal crop load (no. of fruit cm-2 of TCSA) characterized the direct impact of rootstock vigor on peach internal quality. Twenty-five fruits from each rootstock were assessed for maturity [IAD and flesh firmness (FF)] and internal quality [dry matter content (DMC) and soluble solids concentration (SSC)]. Physiologically characterized peach fruit mesocarp was further analyzed by non-targeted metabolite profiling using gas chromatography mass spectrometry (GC-MS). To account for differences in light availability created by the varying levels of vigor, and its influence on the developing fruits internal quality, mid-canopy photosynthetic active radiation transmission (i.e., light availability) was collected across genotypes with a line quantum sensor. DMC and SSC increased significantly with decreasing vigor and increasing light availability, potentially due to reduced intra-tree shading and better light distribution within the canopy. Metabolite distribution was associated with rootstock vigor class, mid-canopy light availability and fruit quality characteristics. Fructose, glucose, sorbose, neochlorogenic and quinic acids, catechin and sorbitol were associated with high light environments and enhanced quality traits, while sucrose, butanoic and malic acids related to low light conditions and inferior fruit quality. These outcomes show that while rootstock genotype and vigor are influencing peach tree productivity and yield, their effect on manipulating the light environment within the canopy also plays a significant role in fruit quality development.
2023-10-26 | MSV000093207 | MassIVE