Malus domestica
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ABSTRACT:
PROVIDER: PRJNA390252 | ENA |
REPOSITORIES: ENA
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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:Blue mold, caused by Penicillium expansum, is responsible for postharvest losses of apple fruit, and threatens human health through production of the potent mycotoxin patulin. No major gene(s) providing resistance have as yet been identified, but recent studies indicate a quantitative control of the disease. An AryANE chip covering 60K apple transcripts was used to identify possible candidate gene(s) that are differentially regulated between resistant and susceptible cultivars upon P. expansum infection. Induction of cell wall related gene (PGIP1), and three genes involved in the ‘down-stream’ flavonoid biosynthesis pathway (CHS, FLS and LDOX), shows the fundamental role of cell wall as an important barrier, and contents of polyphenolic compounds of fruits as a quantitative components in enhancing disease resistance to blue mold. Moreover, exogenous application of Jasmonic acid hormone enhanced the defense mechanism in fruits. This is the first report linking Jasmonic acid and activation of cell wall and flavonoid pathway genes in apple fruit resistance to blue mold. Results provide an initial categorization of genes that are potentially involved in the resistance mechanism, and should be useful for developing tools for gene marker-assisted breeding of apple cultivars with an improved resistance to blue mold. SUBMITTER_CITATION: Ahmadi-Afzadi, M., Orsel Baldwin, M., Pelletier, S., Cournol, M., Proux-Wéra, E., Nybom, H., Renou, J.-P. (2018). Genome-wide expression analysis suggests a role for jasmonates in the resistance to blue mold in apple. Plant Growth Regulation, 85 (3), 375-387. , DOI : 10.1007/s10725-018-0388-2
2018-06-01 | GSE99966 | GEO
Project description:Apple leaf spot caused by the Alternaria alternata f. sp. mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA)-mediated small RNAs, MdhpRNA277, from apple (cv. ‘Golden Delicious’) that is induced by infection with ALT1. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five R genes, MdRNL1, MdRNL2, MdRNL3, MdRNL4, and MdRNL5, that are expressed at high levels in the resistant apple variety ‘Hanfu’ and at low levels in the susceptible variety ‘Golden Delicious’ following ALT1 infection. MdhpRNA277 is strongly induced in ‘Golden Delicious’ but was not induced in ‘Hanfu’ following ALT1 inoculation. The promoter activity of MdhpRNA277 was much stronger in ‘Golden Delicious’ than in ‘Hanfu’ after ALT1 inoculation. We identified a single nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between the susceptible variety ‘Golden Delicious’ (pMdhpRNA277-GD) and resistant variety ‘Hanfu’ (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF. Transgenic ‘GL-3’ apple lines expressing pMdhpRNA277-GD: MdhpRNA277 were more susceptible to ALT1 infection than were those expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and low levels of expression of the five target R genes. The failure of MdWHy to bind to pMdhpRNA277-HF might contribute to the low levels of MdhpRNA277 and mdm-siR277-1/-2 expression and the high levels of R gene expression and resistance to Alternaria leaf spot in resistant apple varieties. We confirmed that the SNP in pMdhpRNA277 is associated with Alternaria leaf spot resistance by analyzing the progeny of three additional crosses. The SNP identified in this study could be used as a marker to distinguish between apple varieties that are resistant or susceptible to Alternaria leaf spot.
2018-12-25 | GSE115664 | GEO
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:Comparative transcriptome analysis of apple cultivars
| PRJDB16689 | ENA
Project description:The aim of our study was to decipher differences in the response of a lowly virulent E. amylovora strain to infection of susceptible and resistant apple cultivars at the transcriptome level. For this purpose, we applied an RNA-seq technique to see the global changes in gene expression of E. amylovora while interacting with two apple cultivars at two time points after inoculation of shoots. Additionally, we compared transcriptomes of E. amylovora growing on a microbiological medium and in planta to elucidate transcriptional changes in bacterial cells induced by the host plant environment.
2018-05-01 | E-MTAB-5630 | biostudies-arrayexpress
Project description:malus domestica infected with Penicillium expansum PEXP creA mutant and PhloeR Raw sequence reads
| PRJNA434179 | ENA
Project description:Apple pedicel vascular development array Twelvet apple samples. Biological replicates: 2 for each sample, independently grown and harvested.
2014-05-20 | E-GEOD-51727 | biostudies-arrayexpress
Project description:Transcriptomic response of resistant (PI61983 – Malus sieversii) and susceptible (‘Royal Gala’) parents of the GMAL4593 mapping population of apple to blue mold (Penicillium expansum) infection
| PRJNA383305 | ENA
Project description:Apple pedicel vascular development array
2014-05-20 | GSE51727 | GEO