Comparative transcriptional profiling between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana)
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE61631 | GEO | 2015/04/14
SECONDARY ACCESSION(S): PRJNA261709
REPOSITORIES: GEO
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Project description:Analyses of expression differences in flower bud and leaf of scion and rootstock, in homografts of Arabidopsis Gene expression data of unopened developing flower buds and leaves, newly emerged after homografting, from the scion and the rootstock
2015-04-14 | E-GEOD-61631 | biostudies-arrayexpress
Project description:Grafting is a well-established practice for grapevine to facilitate propagation of productive and tolerant cultivars against several stress factors. It is also considered to be a suitable method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. So far, controlling only effect of rootstock over scion was investigated and root-to-shoot transcriptomic alterations were fallowed on the scions or graft interfaces. The objective of this study was to investigate transcriptomic and physiological influence of scion on the rootstock under drought stress. Therefore, drought tolerant 110R rootstock were firstly grafted with sultana seedless and tested under drought stress with its non-grafted counterpart. The results of treatment indicated that grafted 110R performed the highest root elongation under drought. We carried out a microarray based transcriptome analysis on the roots of grafted and non-grafted 110R to explain this drought derived interaction through scion-to-rootstock. The highest expression increase under drought was recorded for sugar (SWEET) and nitrate or di/tri-peptide (NRT1/ PTR FAMILY) transporter proteins. Expression level of these genes was more highly increased in grafted 110R than its non-grafted counterpart. This situation indicated their potential role in drought tolerance and scion/rootstock harmony. Overexpression of these transporters attributed to increased amount of released nutrient and nitrogen source from abscised leaves of sultana seedless under drought. Remobilization of these rich sources was suggested to chance transcriptomic response of rootstocks and enabled much better growth in grafted 110R. Other transcripts annotated to cell wall modification enzymes (chitinases), osmoregulator proteins (dehydrins, proline-glycine rich proteins) and secondary metabolites (stilbene synthase) were also more highly induced in grafted 110R. This is the first report indicating transcriptomic influence of scion on the grapevine rootstocks and representing the genes responsible in scion/rootstock harmony and drought tolerance.
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Project description:This study aimed at investigating the effect in Grapevine of two different rootstocks (1103 Paulsen - P - and Mgt 101-14 - M) in comparison with not grafted plants - F - on the miRNome of berry skin in Pinot noir (clone Entav 115), to explore the influence of rootstock-scion interaction on grape quality. 7-year old grapevine plants were grown in 70-liters, in an open field arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized and were abundantly irrigated. Berry samples (15 per plant, 3 plants per replicate), were collected at two different developmental stage: veraison (1) and maturation (2), and dissected to separate skin tissues. Total RNA was extracted and DNase treated, small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina®), following all manufacturers' instructions. Eighteen bar-coded small RNA libraries were constructed starting from 1 µg of total RNAs.
2020-09-30 | E-MTAB-8756 | biostudies-arrayexpress
Project description:This study aimed at investigating the effect in Grapevine of two different rootstocks (1103 Paulsen - P - and Mgt 101-14 - M) in comparison with not grafted plants - F - on the transcriptome of berry skin in Pinot noir (clone Entav 115), to explore the influence of rootstock-scion interaction on grape quality. 7-year old grapevine plants were grown in 70-liters, in an open field arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized and were abundantly irrigated. Berry samples (15 per plant, 3 plants per replicate), were collected at two different developmental stage: veraison (1) and maturation (2), and dissected to separate skin tissues. Total RNA was extracted from berry skins and DNase treated. 18 mRNA seq libraries were prepared, starting from total RNA (1 µg), using TruSeq RNA sample preparation kit (Illumina), according to manufacturers’ instructions. Libraries were quantified through qRT-PCR, as recommended by the protocol, and single-end sequenced for 100 bases on an Illumina Genome Analyzer (GAIIx).
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Project description:Genotype, climate, soil qualities, and rootstocks are among the main factors that influence grape development as well as fruit and wine composition. In this work, the rootstock/scion interactions were studied using transcriptomic and metabolic approaches on leaves of Gaglioppo variety, grafted onto thirteen different rootstocks growing in the same locations. The experiments were performed in a vineyard in the south of Italy, characterized by the Mediterranean climate with warm and dry summers. Whole leaf transcriptome of ‘Gaglioppo’ grafted on five selected rootstocks showed high variability in gene expression. In particular, significant modulation of transcripts linked to primary (e.g. carbohydrate and transport) and secondary metabolism (e.g. phenylpropanoids pathways and response to stress) was observed. Interestingly, genes involved in the priming defense responses (e.g stilbenes and defense genes) were strongly activated in some graft combinations. These results were further confirmed by the quantification of stilbene contents. According with these observations, the leaves of ‘Gaglioppo’ grafted on 1103 Paulsen showing the lowest levels of stilbene synthase transcripts and stilbene metabolites, reveal the greater sensitivity to downy mildew in in vitro assay. This study carrying out an extensive analysis of rootstock effects to scion leaves open a useful way to unravel this complex interaction
2017-06-12 | GSE82317 | GEO
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.
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Project description:Rootstock genotype has been characterized as influential on the scion development. A similar process may be expected in the opposite direction. Therefore, we carried out a RNA-Seq analysis of two peach x almond hybrid roostock samples grafted with two different almond commercial cultivars in one-year ald scion/rootstock combinations, while also analyzing the effect of the rootstock genotype on scion samples.
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Project description:Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought tolerant) or 125AA (drought sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100 % veraison. The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signalling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA concerning genes related to jasmonate, phenylpropanoid metabolism and PR-proteins. The data also suggests a link between jasmonate and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and jasmonate are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties.
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