Elucidating the role of polygalacturonase genes in strawberry fruit softening
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ABSTRACT:
PROVIDER: PRJEB36434 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3841730_1.fastq.gz | Fastqsanger.gz | |||
| ERR3841730_2.fastq.gz | Fastqsanger.gz | |||
| ERR3841731_1.fastq.gz | Fastqsanger.gz | |||
| ERR3841731_2.fastq.gz | Fastqsanger.gz | |||
| ERR3841722_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study was to determine the role of genes encoding polygalacturonases in strawberry fruit softening. To this purpose, several transgenic lines, cv. Chandler, were generated: plants with PG genes FaPG1 or FaPG2 downregulated, alone or in combination, by antisense transformation. Plants were grown in a confined greenhouse and fruits were harvested at the stage of full ripeness (100% of fruit surface red). The results obtained indicate that the silencing of these genes reduced fruit softening at similar level but there is not a sinergistic effect on fruit firmness.
2021-01-21 | E-MTAB-8736 | biostudies-arrayexpress
Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.
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Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.
2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress
Project description:With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.
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Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.
2018-11-13 | GSE113084 | GEO
Project description:For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.
2021-05-17 | GSE167183 | GEO
Project description:To determine the effect of different temperature on strawberry after harvest, physiological indicator analysis and proteomics analysis were conducted on ripened strawberry (‘Sweet Charlie’) fruit stored at 4 °C, 23 °C, and 37 °C (±2) for 10 or 20 days. Results showed that 4 °C maintained a better visual quality of strawberry, and the weight loss and firmness remained stable within 3 days. Low temperature negatively affected anthocyanin but positively affected soluble sugars. Though anthocyanin content was higher with increasing temperature, anthocyanin synthesis related proteins were downregulated. Higher indole-acetic acid (IAA) content in seeds and lower abscisic acid (ABA) content were found in berry at 4 °C. Antioxidant related proteins were upregulated during storage, showing a significant up-regulation of POD at 4 °C, and AsA-GSH cycle related proteins and heat shock proteins (HSPs) at 37 °C. In addition, overexpressed sugar phosphate/phosphate translocator, 1-aminocyclopropane-1-carboxylate oxidase and aquaporin PIP2-2 had a positive effect in response to low temperature stress for containing higher protopectin content and POD activity.
2022-02-07 | PXD030184 | Pride
Project description:The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaPRE1, a non-DNA-binding bHLH transcription factor. FaPRE1 is a ripening-related transcription factor that regulates genes involved in cell architecture in strawberry fruit receptacles.
2019-10-18 | GSE125995 | GEO
Project description:The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaDOF2, a DOF-type transcription factor. FaDOF2 is a ripening-related transcription factor that regulates key genes involved in eugenol biosynthesis in strawberry fruit receptacles.
2018-07-31 | GSE94606 | GEO
Project description:Genetic improvement of tomato by targeted control of fruit softening. Uluisik et al. Nature Biotechnology (2016) doi:10.1038/nbt.3602
| PRJEB13836 | ENA