Auto-grafting in grapevine 3 and 28 days after grafting
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
SUBMITTER: Sarah Cookson
PROVIDER: E-MEXP-3803 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The transcriptional response in the shoot apex to hetero-grafting Cabernet Sauvignon (CS) with the rootstocks 1103 Paulsen (CS/1103P) and Riparia Gloire de Montpellier (CS/RG) compared to the auto-grafted control (CS/CS) four months after grafting. Gene expression profiling was done using the Nimblegen whole genome array with 4 biological replicates of 5 pooled shoot apices.
2014-01-11 | E-MTAB-1523 | biostudies-arrayexpress
Project description:Transcriptional changes occurring at the graft interface of auto- (Cabernet Sauvignon/ Cabernet Sauvignon) and hetero-grafted (Cabernet Sauvignon/ Riparia Gloire de Montpellier and Cabernet Sauvignon /1103 Paulsen) grapevine. Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates of 15 pooled graft interfaces harvested 3, 7, 14 and 28 d after grafting.
2014-04-09 | E-MTAB-1610 | biostudies-arrayexpress
Project description:Phytophthora blight is a highly destructive soil borne disease caused by Phytophthora capsici Leonian, which seriously threatens global pepper production. Grafting is one of the important means to improve plant disease resistance and prevent soil borne diseases in vegetable production. However, the molecular mechanism by which grafting enhances the resistance of pepper to Phytophthora blight is still unclear. This study used Phytophthora capsici resistant strain ‘ZCM334’ and susceptible strain ‘Early Calwonder’ as rootstocks, and ‘Early Calwonder’ as scions for grafting. Phenotypic observation and cytological analysis showed that compared with the ‘Early Calwonder’ self rooted plants, the ‘ZCM334’ grafted plants had a later onset of disease, stronger resistance, and less damage to leaf cells, indicating that grafting can significantly improve the resistance of pepper to Phytophthora capsici. This study identified differentially expressed proteins (DEPs) in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants through proteomic analysis based on iTRAQ technology, and 478 and 349 DEPs were identified between their leaves and roots, respectively. These DEPs were mainly involved in metabolic process, cellular process, response to stimulus and catalytic activity processes. We identified and screened 12 DEPs with consistent expression trends in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants, including seven DEPs related to Phytophthora capsici resistance (CA01g31060, CA02g15780, CA02g30850, CA01g11410, CA05g12260, CA03g35150, and CA03g36980) and five proteins with unknown functions (CA01g26190, CA11g10620, CA12g02730, CA01g20890 and CA02g11340). Through qRT-PCR analysis, a significant correlation was observed between the protein and transcript levels of these 12 DEPs, and their expression characteristics were analyzed in the roots and leaves of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants at different stages (0h, 12h, 24h, and 36h) after inoculation with Phytophthora capsici. This study provides valuable information for exploring the molecular mechanisms by which grafting enhances the resistance of pepper to Phytophthora blight and the excavation of these key genes provides research ideas for studying the regulatory network of pepper resistance to Phytophthora capsici.
2024-05-24 | PXD045628 | Pride
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: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:Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. Stem cross-sections showed intensely dividing cells forming root primordial. One to two days later the bark split and the organized sequence of cell division and differentiation steps in the primordium led to the establishment of the main root tissues, as well as the vascular connections of the incipient root with the pre-existing stem vasculature. Subsequently, the outgrowth and emergence of the adventitious root occurred. We refer to the dormant cutting as stage 0, the organizing primordium as stage 1, the primordium differentiation as stage 2. To examine changes in gene transcription associated with the development of adventitious roots, we monitored the transcript levels in differentiating primordia using microarrays. cDNA was prepared from replicate sets of P. trichocarpa rooted cuttings harvested at stages 0, 1 and 2. The Populus whole-genome expression array version 2.0 manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P. trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturers instructions. We carried out nine hybridizations (NimbleGen) with samples derived from three early developmental stages of P. trichocarpa adventitious roots. cDNA was synthesized using CLONTECH Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.
2012-11-01 | E-GEOD-34096 | biostudies-arrayexpress
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:Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples. In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics. The antibiotic treatments were conducted on the randomized complete block design with three replicates. For each replicate, 15 scions were treated in each antibiotic treatment (Amp and Gm) and control (CK1 and CK2). HLB-affected budsticks were sampled from severely HLB-affected field rough lemons (cv. Lemon #76) at the USDA-ARS-USHRL farm in Fort Pierce, FL and tested positive for Las by real-time qPCR. They were soaked in the antibiotic treatments; ampicillin sodium at a concentration of 1.0 g/L (Amp, Sigma-Aldrich, St. Louis, MO) or gentamicin sulfate at a concentration of 100 mg/L (Gm, Sigma-Aldrich, St. Louis, MO) and water as the diseased control (CK1), overnight in a fume hood under ventilation and lighting. Las-free budsticks, which tested negative by qPCR from healthy rough lemons, were also soaked in water as the healthy control (CK2). The budsticks were grafted onto two-year-old healthy grapefruit (Citrus paradisi 'Duncan') rootstocks and covered using plastic tape for three weeks. To improve scion growth, new flush from the rootstocks was removed after grafting and then allowed to grow. All experimental plants were grown in an insect-proof greenhouse. The first leaf samples from scions (rough lemon) and rootstocks (grapefruit) for DNA extraction were taken four months after inoculation, and second samplings were taken at six month after inoculation. The leaves were washed in tap water and then rinsed three times with sterile water. The midribs of the leaves were excised, frozen in liquid nitrogen, and stored at -80M-BM-0C. The midribs of five leaves from each sample were pooled, and DNA was isolated for qPCR analysis for Las bacterium. DNA from the leaf midribs of scions for the PhyloChipT G3 analysis, which was extracted from all samples of the same treatment, was pooled in equal amounts and quantified by the PicoGreenM-BM-. method. The PhyloChipTM G3 analysis was conducted by Second Genome Inc. (San Francisco, CA).
2013-05-09 | E-GEOD-46728 | biostudies-arrayexpress
Project description:Tieguanyin (TGY) and Shuixian (SX) cultivars of Camellia sinensis were selected to explore the mechanism underlying the accumulation of the rare earth element lanthanum through proteomics. Roots and fresh leaves of TGY and SX with low- and high-accumulation potential for lanthanum, respectively, were studied; 845 differentially expressed proteins (DEPs) were identified. Gene ontology analysis showed that the DEPs are involved in redox processes and related to molecular functions, such as defense and oxidative stress reactions, catalytic activity, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis showed that DEPs were associated with glutathione (GSH) and α-linolenic acid metabolism, plant pathogen interaction, and oxidative phosphorylation. Thirty-seven proteins in the GSH metabolism pathway showed significant differences, of which 18 GSH S-transferases show differential expression patterns in the root system.The expression multiples of GST (TEA004130.1) and GST (TEA032216.1) in T1L and T0L were 6.84 and 4.06, respectively, which were significantly higher than those in S1L and S0L. The lanthanum-induced activation of the GSH-related antioxidant defense system may cause the difference in TGY and SX. The LOX2.1 (TEA011765.1) and LOX2.1 (TEA011776.1 expression ratios) in the α-linolenic acid metabolic pathway were 2.44 and 6.43 in T1R and T0R, respectively, which were significantly higher than those in S1R snd S0R. The other differential proteins were also sig-nificantly upregulated in TGY leaves.The synthesis of specific substances induces lantha-num-associated defense responses in TGY, which is of great significance for the stability of its yield.
2023-03-11 | PXD039195 | Pride
Project description:This study evaluated the transcriptional reprogramming of a susceptible genotype (Pera sweet orange) challenged with the pathogenic bacteria Candidatus Liberibacter americanus (CaLam), using a customized 385K microarray containing about 32,000 unigene transcripts. For the microarray experiment were used symptomatic leaves from two Pera sweet orange plants inoculated with either bark or bud pieces infected with Candidatus Liberibacter americanus and two non-infected control plants.
2012-12-17 | E-GEOD-41221 | biostudies-arrayexpress