Malus domestica
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ABSTRACT:
PROVIDER: PRJDB16689 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide DNA methylation analysis between long-term in vitro shoot culture and acclimatized apple plants DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material. Significant differences in DNA methylation were identified in 586 out of 45,116 genes, including promoter and coding sequences, and classified as differentially methylated genes (DMGs). Differential methylation was visualised by an MA plot and functional genomic maps were established for biological processes, molecular functions and cellular components. Considering the DMGs, in vitro tissue culture resulted in the highest level of methylation, which decreased after acclimatization and tended to be similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2GO v5.1.12 for Gene Ontology. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying gene expression.
2019-07-25 | GSE116995 | GEO
Project description:Global gene expression analysis of resistant and susceptible apple cultivars challenged with Penicillium expansum
| PRJNA390252 | ENA
Project description:Apple is typically stored under low temperature and controlled atmospheric conditions to ensure a year round supply of high quality fruit for the consumer. During storage, losses in quality and quantity occur due to spoilage by postharvest pathogens. One important postharvest pathogen of apple is Botrytis cinerea. The fungus is a broad host necrotroph with a large arsenal of infection strategies able to infect over 1,400 different plant species. We studied the apple-B. cinerea interaction to get a better understanding of the defense response in apple. We conducted an RNAseq experiment in which the transcriptome of inoculated and non-inoculated (control and mock) apples was analyzed at 0, 1, 12 and 28 h post inoculation. Our results show extensive reprogramming of the apple's transcriptome with about 28.9 % of expressed genes exhibiting significant differential regulation in the inoculated samples. We demonstrate the transcriptional activation of pathogen-triggered immunity and a reprogramming of the fruit’s metabolism. We demonstrate a clear transcriptional activation of secondary metabolism and a correlation between the early transcriptional activation of the mevalonate pathway and reduced susceptibility, expressed as a reduction in resulting lesion diameters. This pathway produces the building blocks for terpenoids, a large class of compounds with diverging functions including defense. 1-MCP and hot water dip treatment are used to further evidence the key role of terpenoids in the defense and demonstrate that ethylene modulates this response.
2022-03-01 | GSE195841 | 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. 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:V. inaequalis causes apple scab disease, the most economically important disease of apples. In this study, we generated a comprehensive RNA-seq transcriptome of V. inaequalis during host colonization of apple, with six in planta time points (12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi) and one in culture reference (fungus grown on cellophane membranes overlaying potato dextrose agar). Analysis of this transcriptome identified five in planta gene expression clusters or waves corresponding to three specific infection stages: early, mid and mid-late infection of subcuticular biotrophic host-colonization. In our analysis we focus on general fungal nutrition (plant cell wall degrading enzymes and transporters) as well as effectors (proteinaceous effectors and secondary metabolites). Early infection was characterized by the expression of genes that encode plant cell wall-degrading enzymes (PCWDEs) and proteins associated with oxidative stress responses. Mid-late infection was characterized by genes that encode PCWDEs and effector candidates (ECs).
2022-03-14 | GSE198244 | GEO
Project description:Purpose: The aim of this study was to identify the specific transcriptomic changes in apple root tissue in response to infection by F. Proliferatum.The characterized transcriptome changes during apple root defense responses to F. Proliferatum inoculation should facilitate the identification of the key molecular components, which may differentiate the resistance and susceptibility among apple rootstock germplasm.
2021-04-09 | GSE171688 | GEO
Project description:Large scale analysis of apple mealiness within IM apple progeny
| PRJNA257178 | ENA
Project description:Large scale analysis of apple development within HIVW apple progeny
| PRJNA270072 | ENA
Project description:Bitter pit is the most important physiological disorder affecting apples. In order to ascertain the genetic bases of its incidence in apple fruit, a mapping population of ‘Braeburn’ (susceptible to bitter pit) × ‘Cameo’ (resistant to bitter pit) cultivars was used to map the trait over two growing seasons. RNA-Seq on pools of RNA extracted from fruits of three resistant and three susceptible to bitter pit progenies at post-fertilization and full maturity stages, permitted us to identify a number of candidate genes underlying genetic resistance/susceptibility to bitter pit.
2018-06-12 | E-MTAB-6190 | biostudies-arrayexpress
Project description:Transcriptome analysis of apple wild type and the transgenic plants
| PRJNA357989 | ENA