Malus domestica
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ABSTRACT:
PROVIDER: PRJNA834559 | ENA |
REPOSITORIES: ENA
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Project description:Background Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection. Results Approximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR. Conclusion RNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08721-3.
| S-EPMC9250749 | biostudies-literature
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:Characterization of Malus x domestica chloroplast proteome
2022-03-01 | PXD009527 | Pride
Project description:Chloroplasts were purified by centrifugation in Percoll gradient from low temperature (4 C), control (22 C) and high temperature (30 C) grown Malus x domestica microshoots. The proteins were digested using filter aided sample processing (FASP) and analyzed using nano-LC MS/MS. Constant scan rate of 2 Hz and range from 100 to 2,200 m/z was used for the MS spectra acquisition. Data-dependent auto-MS/MS method (Compass 1.5 acquisition and processing software, Bruker Daltonics) was used for selecting the 10 most abundant precursor ions for fragmentation. The MS/MS summation time was adjusted based on precursor intensity within the range 1-10 Hz. Active exclusion of already analyzed precursors was used with a release time of 30 s. Precursor ion isolation window and the CID collision energy were adjusted between 3-9 Th and 34-55 eV as a function of the m/z value, respectively. The data files (9 low temperature samples, 12 control samples and 9 high temperature sampes) are described in the "metadata.txt" file.
2019-10-03 | PXD014212 | Pride
Project description:The Alternaria alternata apple pathotype adversely affects apple (Malus domestica Borkh.) cultivation. However, the molecular mechanisms underlying enhanced resistance to this pathogen in apple remain poorly understood. We have previously reported that MdWRKY75 expression is upregulated by A. alternata infection in 'Sushuai' apples. In this study, we discovered that overexpression of MdWRKY75e increased the resistance of transgenic apple lines to A. alternata infection, whereas silencing this gene enhanced susceptibility to A. alternata infection. Furthermore, we found that MdWRKY75e directly binds to the MdLAC7 promoter to regulate the biosynthesis of laccase and increase the biosynthesis of lignin during A. alternata infection. Moreover, the thickening of the cell wall enhanced the mechanical defense capabilities of apple. In addition, we found that jasmonic acid remarkably induced MdWRKY75e expression, and its levels in transgenic apple lines were elevated. These results indicate that MdWRKY75e confers resistance to the A. alternata apple pathotype mainly via the jasmonic acid pathway and that pathogenesis-related genes and antioxidant-related enzyme activity are involved in the disease resistance of MdWRKY75e transgenic plants. In conclusion, our findings provide insights into the importance of MdWRKY75e for resistance to A. alternata infection in apples.
| S-EPMC8502781 | biostudies-literature
Project description:Abstract The EFSA Panel on Plant health was requested to prepare and deliver risk assessments for commodities listed in the relevant Implementing Acts as ‘High risk plants, plant products and other objects’ (Commission Implementing Regulation (EU) 2018/2019 establishing a provisional list of high‐risk plants, plant products or other objects, within the meaning of Article 42 of Regulation (EU) 2016/2031). The current scientific opinion covers all plant health risks posed by dormant bare rooted plants for planting of Malus domestica (1–2 years old) imported from Serbia, considering the available scientific information, including the technical information provided by the Plant Protection Directorate from Serbia on 27 December 2019. The relevance of an EU‐quarantine pest for this opinion was based on evidence that: (a) the pest is present in Serbia; (b) the pest uses M. domestica as a host; (c) one or more life stages of the pest can be associated with the specified commodity. The relevance for this opinion of pests not regulated in the EU was based on the following criteria: (i) the pest is present in Serbia; (ii) the pest is not present in the EU; (iii) M. domestica is a host of the pest; (iv) the pest can be associated with the commodity and (v) the pest may have an impact and can pose potential risk for the EU territory. After the assessment of 1191 potential pests, one bacterium, Erwinia amylovora, fulfilled all criteria and accordingly, was selected for further evaluation. For this bacterium, the risk mitigation measures proposed in the technical dossier were evaluated. Limiting factors on the effectiveness of the measures were also considered. For the selected species, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on E. amylovora, including any uncertainties. Based on the outcomes of an Expert Knowledge Elicitation, the Panel is considering a pallet as a unit; and taking into account the uncertainties associated with the assessment, the panel is 95% sure that 9,934 or more pallets out of 10,000 will be pest free.
| S-EPMC10464673 | biostudies-literature
Project description:An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
| S-EPMC8942233 | biostudies-literature
Project description:MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes, including flowering, fruit development and nodulation. However, its role in regulating flavonoid biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red coloration and anthocyanin accumulation in various tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and qRT-PCR analyses. The positive role of MdAP2_1a in regulating anthocyanin biosynthesis was supported by the enhanced petal anthocyanin accumulation in transgenic tobacco plants overexpressing MdAP2_1a, and by the reduction in anthocyanin accumulation in apple and cherry fruits transfected with an MdAP2_1a virus-induced-gene-silencing construct. We demonstrated that MdAP2_1a could bind directly to the promoter and protein sequences of MdMYB10 in yeast and tobacco, and enhance MdMYB10 promotor activity. In Arabidopsis, over-expression of miR172 reduced flavonoid (including anthocyanins and flavonols) concentration and RNA transcript abundance of flavonoid genes in plantlets cultured on medium containing 7% sucrose. The anthocyanin content and RNA abundance of anthocyanin genes could be partially restored by using a synonymous mutant of MdAP2_1a, which had lost the miR172 target sequences at mRNA level, but not restored by using a WT MdAP2_1a. These results indicate that miR172 inhibits flavonoid biosynthesis through suppressing the expression of an AP2 transcription factor that positively regulates MdMYB10.
| S-EPMC8846330 | biostudies-literature
Project description:Color is an important trait for horticultural crops. Carotenoids are one of the main pigments for coloration and have important implications for photosynthesis in plants and benefits for human health. Here, we identified an APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factor named MdAP2-34 in apple (Malus domestica Borkh.). MdAP2-34 expression exhibited a close correlation with carotenoid content in 'Benin Shogun' and 'Yanfu 3' fruit flesh. MdAP2-34 promotes carotenoid accumulation in MdAP2-34-OVX transgenic apple calli and fruits by participating in the carotenoid biosynthesis pathway. The major carotenoid contents of phytoene and β-carotene were much higher in overexpressing MdAP2-34 transgenic calli and fruit skin, yet the predominant compound of lutein showed no obvious difference, indicating that MdAP2-34 regulates phytoene and β-carotene accumulation but not lutein. MdPSY2-1 (phytoene synthase 2) is a major gene in the carotenoid biosynthesis pathway in apple fruit, and the MdPSY2-1 gene is directly bound and transcriptionally activated by MdAP2-34. In addition, overexpressing MdPSY2-1 in apple calli mainly increases phytoene and total carotenoid contents. Our findings will advance and extend our understanding of the complex molecular mechanisms of carotenoid biosynthesis in apple, and this research is valuable for accelerating the apple breeding process.
| S-EPMC8492665 | biostudies-literature
Project description:The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'). This Scientific Opinion covers plant health risks posed by 1- to 3-year-old dormant grafted plants and rootstocks of Malus domestica imported from Ukraine, taking into account the available scientific information, including the technical information provided by Ukraine. All pests associated with the commodity were evaluated against specific criteria for their relevance for this opinion. Two quarantine pests (Lopholeucaspis japonica and Tobacco ringspot virus), one protected zone quarantine pest (Erwinia amylovora) and one non-regulated pest (Eotetranychus prunicola) that fulfilled all relevant criteria were selected for further evaluation. For Erwinia amylovora, for which special requirements are specified in Commission Implementing Regulation (EU) 2019/2072, Annex X, item 9, the fulfilment of these requirements was evaluated. Based on the information provided in the dossier, the specific requirements for Erwinia amylovora were not met. For the three remaining selected pests, the risk mitigation measures proposed in the technical dossier from Ukraine were evaluated taking into account the possible limiting factors. For the selected pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with Eotetranychus prunicola being the pest most frequently expected on the imported plants. The Expert Knowledge Elicitation indicated with 95% certainty that between 9,912 and 10,000 bundles (consisting of 50 plants each) per 10,000 would be free from Eotetranychus prunicola.
| S-EPMC8585640 | biostudies-literature