Project description:Vitis vinifera RNA degradome Isolated polyadenylated RNA from total RNA extracts of Vitis vinifera leaves, were ligated to 5'-adapter that include san MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
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.
Project description:The objective of the study was to uncover the developmental dynamics in the artificially induced somatic embryogenesis of Vitis vinifera on the transcriptome level.
Project description:Vitis vinifera endogenous small RNAs Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
Project description:Solanum lycopersicum RNA degradome sequencing Isolated polyadenylated RNA from total RNA extracts of Solanum lycopersicum, were ligated to 5'-adapter that includes an MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and ligated to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
Project description:Bud endodormancy induction response of two genotypes (Seyval, a hybrid white wine grape and Vitis riparia, PI588259, a native North American grape species) was compared under long (15 h) and short (13 h) photoperiods. Proteins were extracted from both genotypes for all time points and experimental conditions. The proteins were separaed by 2D-PAGE, trypsin digested, and the peptides identified with a MALDI-TOF-TOF mass spectrometer. A master gel was made and mapped with all proteins from both genotypes. The proteins were identified by matching the peptide sequences against the 8X Vitis vinifera grape genome in NCBI. This study was funded by NSF grant DBI064755 and is the result of a collaboration between Dr. Anne Fennell at South Dakota State University and Dr. Grant R. Cramer at the University of Nevada, Reno.
Project description:Physiological changes in trunk wood of Vitis vinifera L. cv. Chardonnay in response to esca proper and apoplexy revealed by proteomic and transcriptomic analyses