Dataset Information

Identification of microRNAs involved in cold stress response in grapevine.

ABSTRACT: Two small RNA libraries were generated from micropropagated ‘Muscat Hamburg’ (Vitis vinifera) plantlets under normal and low temperatures (4 °C). A total of 163 known miRNAs and 299 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. This study indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE68970 | GEO | 2016/06/14

SECONDARY ACCESSION(S): PRJNA284238

REPOSITORIES: GEO

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Project description:Long distance transfers on genetic material (mRNA, miRNA, Protein, etc.) and metabolites (Hormone) between rootstock and scion is also well documented in the homo-grafting hybrids, but the process in distant-grafting is not reported where rootstock and scion belonging to different Familly. We repeatedly grafted the Vitis vinifera scion onto the Schisandra chinensis stock and got 20 interfamily vegetative hybrids ― Vitis vinifera / Schisandra chinensis (Vs) that could grow normally over 25 years. We found the phonotype leaf, internode, fruit of Vs upper the graft union transformed to intermediate stage between V. vinifera and S. chinensis, and the new traits was inherited by vegetative propagation. To expose the reason, using the simultaneous self-rooted Vitis vinifera (Vv) as control, differences of transcriptomics, miRNAs, degradome between Vv and Vs were analyzed by high-throughput sequencing, and the metabolome by liquid Chromatograph Mass Spectrometer (LC-MS). The results showed that a total of 2113 differentially expressed genes (DEGs), GO annotation and KEGG pathway enrichment analysis found that DEGs function mainly included oxidation-reduction process, metabolic process, etc. 79 differentially expressed miRNAs (DEMs) contains 27 known miRNAs and 52 novel miRNAs were identificated, the main functions of DEMs were defense response, biosynthetic process, etc. The target gene detected by degradome sequencing were mainly regulation of transcription & DNA-templated, auxin-activated signaling pathway, etc. And the degradation group detected 840 target genes corresponding to 252 miRNAs, of which 12 DEMs and the corresponding target gene expression levels were mostly negatively correlated. Meanwhile, 1188 differentially metabolic compounds were identified, the most common of which were sputum metabolism, arginine and proline metabolism, and ABC transporters. Especially the metabolites schizandrin was significantly down regulated and gomisin was up regulated in Vs that were main medicinal ingredients in Schisandra. KEGG pathway enrichment analysis of differential metabolites found more than 30 differential metabolic pathways of Vv-Vs. Our data demonstrate the impact of interfamily graft on the genetic materials and metabolites for the scion and the traits can stable inherited by vegetative propagation, providing an important reference and basis for future breeding through select target gene type rootstocks.

Dataset Information

Identification of microRNAs involved in cold stress response in grapevine.

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