Ontology highlight
ABSTRACT:
PROVIDER: PRJNA549998 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9333721_1.fastq.gz | Fastqsanger.gz | |||
| SRR9333721_2.fastq.gz | Fastqsanger.gz | |||
| SRR9333722_1.fastq.gz | Fastqsanger.gz | |||
| SRR9333722_2.fastq.gz | Fastqsanger.gz | |||
| SRR9333723_1.fastq.gz | Fastqsanger.gz |
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Project description:Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 411 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substanial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected. We also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Overall, our work provide important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributed to the fruit skin color formation.
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Project description:miRNAs were important regulators involving in plant-pathogen interactions. However, their roles in apple response to Valsa canker pathogen (Valsa mali, Vm) infection were poorly understood. In this study, we constructed two miRNA libraries using the bark tissues of apple twig (Malus domestica Borkh “Fuji”) inoculated with Vm (IVm) and PDA medium (control, BMd). Among the all miRNAs, 23 miRNAs were specifically isolated in BMd and 39 miRNAs were specifically isolated in IVm. Compared with BMd, the expression of 294 miRNAs decreased, and 172 miRNAs increased in IVm, respectively. We also identified the target genes of these miRNAs using degradome sequencing technology. In total, 353 differentially expressed miRNAs during the pathogen infection were detected to target 1 077 unigenes with 2 251 cleavage sites. Based on GO and KEGG analysis, the genes were found to be mainly related to transcription regulation and signal transduction. We further selected 17 miRNAs and 22 corresponding target genes to detect the expression profiles during pathogen infection. The results indicate that most of them are involved in apple twig-Vm interaction. What’s more, miRNAs and their corresponding target genes seem to regulate the apple twig-Vm interaction by forming many complicated regulation networks. It is worth that a conserved miRNAs mdm-miR482b, which was down regulated in IVm compared with BMd, has 14 potential target genes, and most of them were disease resistance related genes. More important, the feedback regulation of sRNA pathway in apple twig was much more complex and critical in the interaction between apple bark tissue and V. mali. The results provide insights into the crucial functions of miRNAs in the woody plant, apple tree-Vm interaction.
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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.
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