Comparative transcriptomic analysis of peach fruits in common and high temperature conditions
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ABSTRACT:
PROVIDER: PRJNA506721 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8239740_1.fastq.gz | Fastqsanger.gz | |||
| SRR8239740_2.fastq.gz | Fastqsanger.gz | |||
| SRR8239750_1.fastq.gz | Fastqsanger.gz | |||
| SRR8239750_2.fastq.gz | Fastqsanger.gz | |||
| SRR8239741_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: This study was to explore the underlying molecular mechanism of temperature effects on fruit quality during shelf life. The transcriptome data of peach fruits stored in high temperature (HT, 35 °C) and common temperature (CT, 25 °C) conditions were measured and compared. Methods: Red flesh peach (Prunus persica L. Batsch cv. Tianxianhong) fruits with consistent color, shape and weight were selected and kept at 5 °C for 2 days after the day of harvest. Then, these fruits were randomly divided into two groups. One group was stored at CT for 7 days, and the other was stored at HT for 7 days. During storage, fruits were sampled at day 1, 2 and 3 as early stage as well as day 5, 6 and 7 as later stage. Total RNA of each sample was extracted and used to construct 24 RNA libraries. RNA sequencing was performed on an Illumina HiSeq 2500 platform. The differences in transcriptome, ethylene production, pulp softening of postharvest peach fruits were compared between CT and HT storage conditions Results: Our results showed that HT conditioning after 5 °C is better than CT to maintaining fruit quality during shelf life due to MEKK1-MKK2-MPK4/6 signal transduction and low level of ethylene and auxin biosynthesis enzymes which may affect genes related to softening and membrane stability through ethylene response factors (ERFs) and auxin response factors (ARFs).
2020-06-27 | GSE122868 | GEO
Project description:Mummified peach fruits metagenome and metatranscriptome
| PRJNA624910 | ENA
Project description:A transcriptome analysis was applied on two peach (Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify cold-responsive genes that might be involved in tolerance to long low temperature storage. Peach fruit from ‘Morettini No2’ and ‘Royal Glory’, a sensitive and a tolerant, to chilling injury cultivars, respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (25°C) or subjected to 4 and 6-weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. Microarray experiments, employing the peach microarray platform (μ PEACH 1.0), were carried out by comparing harvested fruit against 4- and 6-week cold-stored fruit. The analysis identified 173 and 313 genes that were differentially expressed in ‘Morettini No2’ and ‘Royal Glory’ fruit after 4 weeks, respectively. However, the 6 weeks cold storage provoked a decrease in the total number of genes differentially expressed in both cultivars. RNA blot analysis validated the differential expression of certain genes showed in microarray data. Among these genes, two heat shock proteins (hsps), a putative β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related protein PR-4B precursor were induced during cold storage in both cultivars. The induction of hsps and the putative β-D-xylosidase appeared to be independent on the duration of postharvest treatment. On the other hand, transcript levels of lipoxygenase were quite constant during postharvest ripening, while a strong reduction or disappearance was observed after cold storage. A dehydration-induced RD22-like protein showed a reduction in the accumulation of transcripts during postharvest ripening independently on the temperature conditions. Overall, the current study shed some light on the molecular aspects of cold stress in peach fruit quality and identified some ripening and/or cold-induced genes which function need further elucidation.
2011-08-26 | GSE18280 | GEO
Project description:Storage at low temperatures is one of the most used methods to prolong the life of postharvest peaches (Prunus persica (L) Batch.). However, fruit quality is adversely affected by the development of woolliness, a physiological disorder that is apparent when the fruit is ripened after prolonged periods of cold storage and is mainly manifested as loss of juice in the peaches. The aim of this study was to obtain a more detailed cohort of genes that underlie the wolliness in a segregating population with contrasting phenotypes of mealiness after being exposed to cold storage at 4 °C. For this, a transcriptomics approach was applied to fruits from a progeny of individuals accounted for 6% more juicy and woolly 6% over a 2 years. Our results suggest that not only genes related to the maintenance of cell wall architecture may contribute to the development of mealy phenotype. Based on its possible physiological process and differential pattern of expression transcriptomic profiles show that genes related to maintenance (modification I) and membrane fluidity account for the differences between fruits that exhibit contrasting phenotypes of mealiness. These genes may contribute to tolerance to cold during storage. We analyzed a total of 9 woolly fruits (from 3 different trees, 3 fruits from each tree) and 12 juicy fruits (from 4 different trees, 3 fruits from each tree). An RNA pool from 9 woolly fruits was used as reference and was compared to an RNA pool of 3 juicy fruits from each individual tree. Two technical replicates were done for each comparison, thus making in total 8 hybridizations.
2011-10-25 | E-GEOD-33027 | biostudies-arrayexpress
Project description:The fruit of melting-flesh peach cultivars produce high levels of ethylene caused by high expression of PpACS1, resulting in rapid fruit softening at the late-ripening stage. In contrast, the fruit of stony hard peach cultivars do not soften and produce little ethylene due to low expression of PpACS1. To elucidate the mechanism for suppressing PpACS1 expression in stony hard peaches, a microarray analysis was performed. Several genes that displayed similar expression patterns as PpACS1 were identified and shown to be IAA-inducible genes. Change in gene expression according to growth of fruits in 'melting peach M-bM-^@M-^XAkatsukiM-bM-^@M-^Y fruit sampled at 92, 98, 104 and 106 day after full bloom (DAB). Propylene induced gene expression stony peach M-bM-^@M-^XManamiM-bM-^@M-^Y and M-bM-^@M-^XOdorokiM-bM-^@M-^Y harvested at commercial maturity (Tatsuki et al., 2006).
2013-03-27 | E-GEOD-45490 | biostudies-arrayexpress
Project description:Storage at low temperatures is one of the most used methods to prolong the life of postharvest peaches (Prunus persica (L) Batch.). However, fruit quality is adversely affected by the development of woolliness, a physiological disorder that is apparent when the fruit is ripened after prolonged periods of cold storage and is mainly manifested as loss of juice in the peaches. The aim of this study was to obtain a more detailed cohort of genes that underlie the wolliness in a segregating population with contrasting phenotypes of mealiness after being exposed to cold storage at 4 °C. For this, a transcriptomics approach was applied to fruits from a progeny of individuals accounted for 6% more juicy and woolly 6% over a 2 years. Our results suggest that not only genes related to the maintenance of cell wall architecture may contribute to the development of mealy phenotype. Based on its possible physiological process and differential pattern of expression transcriptomic profiles show that genes related to maintenance (modification I) and membrane fluidity account for the differences between fruits that exhibit contrasting phenotypes of mealiness. These genes may contribute to tolerance to cold during storage.
2011-10-26 | GSE33027 | GEO
Project description:BACKGROUND: Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors. RESULTS: We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold. CONCLUSION: These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.
| S-EPMC2748099 | biostudies-literature
Project description:Thinning is indispensable practice in peach cultivation aiming to reduce fruit number per plant, promoting sink-source balance and reducing competition among fruit, which results in bigger fruit and the improvement of other fruit-quality parameters. Inhibition of floral induction by GAs has been largely demonstrated and commercial products based on GAs have been used to this aim. We tested a product GA4/7 based in different moments after full bloom in peach to reduce the number of flowers in the following season. Return to bloom and transcriptome analysis were performed to identify the best moment for the treatment, increasing the product efficacy and understanding the product action at genetic level.
2024-06-25 | GSE247681 | GEO