Ontology highlight
ABSTRACT:
PROVIDER: PRJNA411951 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6065910_1.fastq.gz | Fastqsanger.gz | |||
| SRR6065910_2.fastq.gz | Fastqsanger.gz | |||
| SRR6065920_1.fastq.gz | Fastqsanger.gz | |||
| SRR6065920_2.fastq.gz | Fastqsanger.gz | |||
| SRR6065911_1.fastq.gz | Fastqsanger.gz |
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Project description:Grafting is an ancient cloning method that has been used widely for thousands of years in agricultural practices. However, the molecular mechanisms for graft union development are still largely unknown. The developmental stage of graft union was characterized based on micrografting method. Microarray data revealed a signal exchange process between cells of scion and stock at 1dag, which reestablished the communication network in graft union. This process was concomitant with the cleaning of cell debris, and both of the processes were initiated by a wound-induced program. The results demonstrate the feasibility and potential power of investigating various plant developmental processes by this method and represent a primary and significant step in interpretation of the molecular mechanisms underlying graft union development. WT/WT seedling grafts of 22-26 hours after grafting were collected for microarray, intact WT seedlings and ungrafted scions and stocks were as control. All three types of sample, grafts (marked as A: whole graft), ungrafted scions and stocks (marked as B: mixture of ungrafted scions and stocks) and intact seedlings (marked as C: whole seedling), were collected at the same time of 22-26 hours after grafting. For sample B, scions and stocks were cut at the same time during grafting. For sample C, intact seedlings were also reserved during grafting. Data were firstly compared between sample A and C, differential expressed probe sets were than tested based on A and B to obtain graft-specific probes.
2012-05-02 | E-GEOD-36447 | biostudies-arrayexpress
Project description:Grafting is an ancient cloning method that has been used widely for thousands of years in agricultural practices. However, the molecular mechanisms for graft union development are still largely unknown. The developmental stage of graft union was characterized based on micrografting method. Microarray data revealed a signal exchange process between cells of scion and stock at 1dag, which reestablished the communication network in graft union. This process was concomitant with the cleaning of cell debris, and both of the processes were initiated by a wound-induced program. The results demonstrate the feasibility and potential power of investigating various plant developmental processes by this method and represent a primary and significant step in interpretation of the molecular mechanisms underlying graft union development.
2012-05-03 | GSE36447 | GEO
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:Hickory (Carya cathayensis) is a woody plant with high nutritional and economic value, and is widely cultivated in China. It is different from herbaceous plants and undergoes a long vegetative stage before reaching floral transition. Hickory can be cultivated on a large scale using grafting. To reveal the response mechanisms to grafting, we employed a proteomics-based approach to identify differentially expressed proteins during the hickory grafting process. In our study, 3723 proteins were identified and 2518 proteins were quantified. A total of 710 differentially quantified proteins (DQPs) were identified and these were involved in various molecular functional and biological processes. Among these DQPs, 341 were up-regulated and 369 were down-regulated at 7 days after grafting compared to the control. The protein interaction networks of the DQPs indicated that there were two enriched interaction clusters. These were „ribosome‟ and „starch and sucrose metabolism‟. Four auxin-related proteins were down-regulated, which was in agreement with the transcription levels of their encoding genes. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the „Flavonoid biosynthesis‟ pathway was significantly up-regulated. Further experiments verified a significant increase in the total flavonoid contents in scions, which suggested that graft union formation may activate flavonoid biosynthesis to increase the contents of a series of downstream secondary metabolites. This comprehensive analysis provides fundamental information on the candidate proteins and the secondary metabolism pathways involved in the grafting process for hickory.
2018-10-26 | PXD006025 | Pride
Project description:Citrus and most other fruit crops are commercially propagated via grafting, which ensures trees have consistent fruit traits combined with favorable traits from the rootstock such as soil adaptability, vigor, and resistance to soil pathogens. Breeding new rootstocks requires careful agronomic evaluations, and widespread use of new rootstocks and scions requires graft compatibility with commercially important scions and rootstocks. Graft incompatibility can occur when the scion and rootstock are not able to form a permanent, healthy union. Understanding and preventing graft incompatibility is therefore of paramount importance in the breeding of new fruit cultivars and in the choice of scion and rootstock by growers. The rootstock US-1283 is a citrandarin generated from a cross of ‘Ninkat’ mandarin (Citrus reticulata) and ‘Gotha Road’ #6 trifoliate orange (Poncirus trifoliata). It was released in 2014 after years of field evaluation because of its superior productivity and good fruit quality on ‘Hamlin’ sweet orange (C. sinensis) under Florida’s growing conditions. Subsequently, it was observed that trees of ‘Bearss’ lemon (C. limon) and ‘Valencia’ sweet orange (C. sinensis) grafted onto US-1283 exhibited apparent incompatible and unhealthy growth near the graft union. The incompatibility manifested as stem grooving and necrosis underneath the bark on the rootstock side of the graft. A genetically similar citrandarin rootstock, US-812 (C. reticulata ‘Sunki’ × P. trifoliata ‘Benecke’), is fully graft compatible with the same scions. Transcriptome analysis was performed on the vascular tissues above and below the graft union of compatible US-812 and incompatible US-1283 graft combinations with ‘Bearss’ and ‘Valencia’ to identify expression networks associated with incompatibility and help understand the processes and potential causes of incompatibility in citrus. Transcriptional reprogramming was stronger in the incompatible rootstock than in the grafted scions. Functional analysis of the transcriptional events below the graft unions of US-1283 incompatible combinations revealed differentially expression genes (DEGs) associated with oxidative stress and plant defense, among other pathways, similar to a pathogen-induced immune response localized to the rootstock, although no known pathogens were detected in the assayed plants. These changes were not observed above the graft unions.Differentially expressed genes (DEGs) in US-1283, but not the scions, were associated with oxidative stress and plant defense, among others, similar to a pathogen-induced immune response localized to the rootstock. No pathogen infection was detected. It is hypothesized this response could have been triggered by signaling miscommunications between rootstock and scion either through 1) unknown molecules from the scion that were perceived as danger signals by the rootstock, 2) missing signals from the scion or missing receptors in the rootstock necessary for the formation of a healthy graft union, 3) the overall perception of the scion by the rootstock as non-self, or 4) a combination of the above.
2024-07-10 | GSE263656 | GEO
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 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: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
Project description:We report transcripts from tomato:tomato and pepper:pepper self-grafts, and tomato:pepper and pepper:tomato hetergrafts over 4 time points: 24 hours after grafting, 3 days after grafting, 5 day after grafting, and 2 weeks after grafting Examination of 4 graft combinations over 4 time points
2021-08-02 | GSE131700 | GEO