Transcriptional expression of different grafting combinations during healing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA787925 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR17196808_1.fastq.gz | Fastqsanger.gz | |||
| SRR17196808_2.fastq.gz | Fastqsanger.gz | |||
| SRR17196809_1.fastq.gz | Fastqsanger.gz | |||
| SRR17196809_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:Grafting was widely used in pear cultivation as an ancient cultivation technique, the use of rootstocks could improve the resistance of pear trees, make pear trees early fruit. The healing process of plant grafting involves complex signal transduction and material accumulation.We used two different grafting combinations, include ‘Qingzhen D1’ on ‘QAUP-1’ and ‘Qingzhen D1’ on ‘Qingzhen D1’.The samples which are the part of graft union of those two combinations were collected om 1 day, 5 days , 9 days and 30 days after grafting. We performed an in-depth RNA-seq analysis to observe the transcriptional changes that occur during the development of two combinations.
2022-12-10 | GSE190654 | GEO
Project description:The commercial tomato cultivar âKommeetâ was grafted either onto the tomato cultivar âMoneymakerâ (sub-optimal temperature sensitive) or onto the line accession âLA 1777â of the wild tomato species S. habrochaites (sub-optimal temperature tolerant) in a heated glasshouse. Grafted tomato plants were grown in a nutrient film technique system with re-circulating nutrient solution resulting in different root temperature (T), which was either optimal (day and night 25±0.6°C) or sub-optimal (day and night 15±0.4°C) while the air T was optimal (day and night 25±0.6°C) throughout the experimental procedure. After 30 days of differential treatment, differences in growth, physiology, and global gene expression in roots and leaves of all grafting and T combinations were investigated.
2017-06-27 | E-MTAB-4986 | biostudies-arrayexpress
Project description:According to the field observation result, the grafting treatment used in this study was found that 101-14MG rootstocks grafted with Crimson Seedless had a positive influence on fruit coloring. Combined metabolomic and transcriptomic analyses were conducted with different treatment grape of own rooted Crimson Seedless cultivar, and grafted 101-14MG, 110R, SO4 rootstocks with Crimson Seedless cultivar. Peonidin 3-O-glucoside, Delphinidin 3-O-glucoside, Cyanidin 3-O-glucoside, Malvidin 3-O-glucoside, Petunidin 3-O-glucoside were identified as the pigments responsible for the purplish red color peels. The results showed that the grafting material of rootstock 101-14MG could promote the accumulation of anthocyanins in grapefruit in advance. Transcriptome analysis revealed the anthocyanins biosynthetic related genes from the upstream (phenylalanine ammonia-lyase) to the downstream (anthocyanidin 3-O-glucosyltransferase, anthocyanidin synthase) were almost upregulation during anthocyanins increased. However, all these genes were highly expressed in samples G715 (Crimson Seedless/ Crimson Seedless), suggested that self-grafting rootstocks might have an earlier response to fruit color-related metabolism. A transcription factors-scale protein interaction (PPI) analysis showed that MYB4, MYB44, MYB80, and dead-box RNA helicases might be the core regulatory genes. Our results provide global transcriptional changes in grape peel color regulation under different grafting conditions for improving the breeding process.
2024-09-22 | GSE184667 | GEO
Project description:Hickory (Carya cathayensis) is an poplar nut-producing tree with high economic value. To overcome its long juvenile phase, grafting was applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation, a newly identified post-translational modification (PTM), is associated with various cellular processes. However, the regulatory mechanism underlying grafting process of hickory has not been studied at the level of PTM. Here, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in hickory. The succinylation is biased to occur on the cytosolic proteins of hickory, indicating an effect of succinylation on the activities of enzymes associated with cellular metabolism. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. In total, seven heat shock proteins (HSPs) with 11 succinylation sites were identified, and all these HSPs were up-regulated during the grafting process of hickory. Our data suggested that succinylated HSPs might play a role in the tolerance of grafted hickory plants. Our data are basic resources for the functional validation of succinylated proteins and a starting point for investigations into the molecular basis of lysine succinylation in the grafting process of hickory.
2020-05-26 | PXD009584 | Pride
Project description:Transcriptomic analyses for grape peel color regulation under different grafting conditions
| PRJNA765608 | ENA
Project description:The widespread use of plant grafting has enabled different plants to join and combine their best properties to improve stress tolerance, growth and yields. Grafting is commonly performed between closely related eudicots or gymnosperms where mechanisms permit tissue fusion yet limit success as plants become unrelated. To investigate these aspects, we developed a micrografting method using young conifer tree seedlings that enabled divergent conifer members to successfully graft. Conifer grafts showed rapid connection of phloem and xylem at the junction, while a genome-wide transcriptome analysis of the Picea abies (Norway spruce) healing junction revealed differential expression of thousands of genes including those related to auxin response and cell wall biogenesis. We compared these genes to those induced during Arabidopsis thaliana graft healing and found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis revealed that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a central hub during Picea grafting and was also induced during Arabidopsis grafting. Arabidopsis mutants lacking PATs failed to attach tissues or successfully graft, while complementing Arabidopsis PAT mutants with the Picea abies PAT1 homolog could rescue tissue attachment and enhance callus formation. Together, our data demonstrate a competency for young tissues to graft to distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration in eudicots and gymnosperms.
2023-10-01 | GSE231631 | GEO
Project description:The analysis of the genes differentially expressed in the rootstock and the callus 3 and 28 d after grafting in grapevine (Vitis vinifera cv Cabernet Sauvignon) auto-grafts.
2013-05-31 | E-MEXP-3803 | biostudies-arrayexpress
Project description:The widespread use of plant grafting has enabled different plants to join and combine their best properties to improve stress tolerance, growth and yields. Grafting is commonly performed between closely related eudicots or gymnosperms where mechanisms permit tissue fusion yet limit success as plants become unrelated. To investigate these aspects, we developed a micrografting method using young conifer tree seedlings that enabled divergent conifer members to successfully graft. Conifer grafts showed rapid connection of phloem and xylem at the junction, while a genome-wide transcriptome analysis of the Picea abies (Norway spruce) healing junction revealed differential expression of thousands of genes including those related to auxin response and cell wall biogenesis. We compared these genes to those induced during Arabidopsis thaliana graft healing and found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis revealed that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a central hub during Picea grafting and was also induced during Arabidopsis grafting. Arabidopsis mutants lacking PATs failed to attach tissues or successfully graft, while complementing Arabidopsis PAT mutants with the Picea abies PAT1 homolog could rescue tissue attachment and enhance callus formation. Together, our data demonstrate a competency for young tissues to graft to distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration in eudicots and gymnosperms.
2023-10-01 | GSE231632 | GEO
Project description:Tendons are composed of a heterogeneous cell environment, with Scleraxis-lineage (ScxLin) cells being the predominant population. Although ScxLin cells are required for maintenance of tendon homeostasis, their functions during tendon healing are unknown. To this end, we first characterized the spatiotemporal dynamics of ScxLin cells during tendon healing, and identified that the overall ScxLin pool continuously expands up to early remodeling healing phase. To better define the function of ScxLin cells during the late proliferative phase of healing, we inducibly depleted ScxLin cells from day 14-18 post-surgery using the Scx-Cre; Rosa-DTR mouse model, with local administration of diphtheria toxin inducing apoptosis of ScxLin cells in the healing tendon. At D28 post-surgery, ScxLin cell depleted tendons (DTRScxLin) had substantial impairments in structure and function, relative to WT, demonstrating the importance of ScxLin cells during tendon healing. Next, bulk RNAseq was utilized to identify the underlying mechanisms that were impaired with depletion and revealed that ScxLin depletion induced molecular and morphological stagnation of the healing process at D28. However, this stagnation was transient, such that by D56 tendon mechanics in DTRScxLin were not significantly different than wildtype repairs. Collectively, these data offer fundamental knowledge on the dynamics and roles of ScxLin cells during tendon healing.
2022-09-13 | GSE213033 | GEO
Project description:To further development of our gene expression approach to cardiovascular disease, we have employed microarray expression profiling as a discovery platform to identify genes with the potential to distinguish the therapeutic target of the vein graft restenosis following coronary artery bypass grafting. Vein graft samples were obtained from model rats which received external jugular vein-carotid bypass grafting at different postoperative timepoints (n=3/group; day 7, 14 and 28, respectively). Vein samples were also obtained from control rats without vascular grafting (n=3/group; day 0). Time-dependent gene expression profiles were described with microarray analysis. Expression of three lncRNA-mRNA pairs (AF062402-Src, BC091437-Edg1 and BC166461- Mcam) from this signature were quantified in the same RNA samples by real-time PCR, confirming the accuracy of the microarray data.
2020-06-16 | GSE152538 | GEO