Small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA542259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9040110.fastq.gz | Fastqsanger.gz | |||
| SRR9040120.fastq.gz | Fastqsanger.gz | |||
| SRR9040111.fastq.gz | Fastqsanger.gz | |||
| SRR9040121.fastq.gz | Fastqsanger.gz | |||
| SRR9040112.fastq.gz | Fastqsanger.gz |
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Project description:Several pathogens infect grapevine, including viruses and viroids. Considering that there are no effective plant protection treatments against these pathogens and vineyards are cultivated through decades usage of high quality and pathogen-free propagation material (rootstocks and scions) is essential. Although presence of regulated pests is routinely checked using ELISA or rarely RT-PCR, these diagnostics methods can detect only particular pathogens moreover can fail to detect variant strains. High-throughput sequencing of small RNAs can be an effective, alternative method to avoid these disadvantages. Since for production of grafts, pathogen free cultivars and rootstocks must be used, 17 grapevine rootstock plantations and 2 rootstock variety collections were selected for characterisation of their virom by high throughput sequencing of virus derived small RNAs.
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Project description:Grafting is a well-established practice for grapevine to facilitate propagation of productive and tolerant cultivars against several stress factors. It is also considered to be a suitable method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. So far, controlling only effect of rootstock over scion was investigated and root-to-shoot transcriptomic alterations were fallowed on the scions or graft interfaces. The objective of this study was to investigate transcriptomic and physiological influence of scion on the rootstock under drought stress. Therefore, drought tolerant 110R rootstock were firstly grafted with sultana seedless and tested under drought stress with its non-grafted counterpart. The results of treatment indicated that grafted 110R performed the highest root elongation under drought. We carried out a microarray based transcriptome analysis on the roots of grafted and non-grafted 110R to explain this drought derived interaction through scion-to-rootstock. The highest expression increase under drought was recorded for sugar (SWEET) and nitrate or di/tri-peptide (NRT1/ PTR FAMILY) transporter proteins. Expression level of these genes was more highly increased in grafted 110R than its non-grafted counterpart. This situation indicated their potential role in drought tolerance and scion/rootstock harmony. Overexpression of these transporters attributed to increased amount of released nutrient and nitrogen source from abscised leaves of sultana seedless under drought. Remobilization of these rich sources was suggested to chance transcriptomic response of rootstocks and enabled much better growth in grafted 110R. Other transcripts annotated to cell wall modification enzymes (chitinases), osmoregulator proteins (dehydrins, proline-glycine rich proteins) and secondary metabolites (stilbene synthase) were also more highly induced in grafted 110R. This is the first report indicating transcriptomic influence of scion on the grapevine rootstocks and representing the genes responsible in scion/rootstock harmony and drought tolerance.
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Project description:Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C. Plantlets with 4–5 leaves were chosen for use in stress treatments. Experiments were conducted with treatment groups: The control (C, without any chemical treatment), TM (treated with 5 μg mL-1 tunicamycin (TM)) and salt (treated with 400 mM NaCl). Microarray analysis was performed and we investigated transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt- and ER-stress at 6 and 24 hours
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