Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock
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ABSTRACT:
ORGANISM(S): Citrus limonia
SUBMITTER: Jose Colmenero-Flores
PROVIDER: E-GEOD-41311 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Whole-genome duplication, or polyploidy, is common in many plant species and often leads to better adaptation to adverse environmental condition. However, little is known about the physiological and molecular determinants underlying adaptation. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological experiments to study root-shoot communication associated with gene expression studies in roots and leaves were performed. V/4xRL was much more tolerant to water deficit than V/2xRL. Gene expression analysis in leaves and roots showed that more genes related to the response to water stress were differentially expressed in V/2xRL than in V/4xRL. Prior to the stress, when comparing V/4xRL to V/2xRL, V/4xRL leaves had lower stomatal conductance and greater abscisic acid (ABA) content. In roots, ABA content was higher in V/4xRL and was associated to a greater expression of drought responsive genes, including CsNCED1, a pivotal regulatory gene of ABA biosynthesis. We conclude that tetraploidy modifies the expression of genes in citrus roots to regulate long-distance ABA signaling and adaptation to stress. Transcriptional profiling of sweet orange (Citrus sinensis) scion leaves comparing control untreated with water deficit conditions. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological studies showed that V/4xRL was much more tolerant to water deficit than V/2xRL. Global gene expression changes induced by water deficit were monitored in the leaves of V/2xRL and V/4xRL by microarray hybridization. The Citrus genome-wide cDNA microarray was used, which includes 21,081 putative unigenes described in Martinez-Godoy et al. (2008). Two independent microarray hybridization experiments with leaves of the 2x Valencia Delta orange alternatively grafted onto 2x or 4x RL rootstocks were respectively performed. For each experiment, the Cy-labelled cDNA of control leaves was hybridized with labelled cDNA from water-stressed samples. To avoid Cy3 and CY5 dye-related artefacts, control and water-stressed cDNA samples were dye-swapped and used to hybridize four slides corresponding to different combinations of the four biological replicates obtained from every treatment. The microarray hybridizations were performed according to Allario et al. (2011). A GenePix 4000B microarray scanner (Axon Instruments, Inc.) and the GenePix Pro 4.1 acquisition software were used to scan the chips at 5-10 M-BM-5m resolution. Photomultiplier gains for the two channels were adjusted so that the ratio of total intensities was approximately 1 and the percentage of saturated spots was about 1%. High-resolution tiff images were generated and used for quantification of gene expression data. Spot positions were identified on the colour images and quality flags were assigned to individual spots both automatic and manually. Only spots with background-subtracted foreground intensity greater than two in at least one channel were used, and only microarrays with optimal hybridization data were pre-processed and normalized for further analyses. Raw data were imported into the R computing environment for pre-processing, visualization, and statistical analysis. To identify probes showing significant differential gene expression between samples, the Linear Models in Microarrays (LIMMA; Smyth, 2005) software package was used. Pre-processing and normalization of two-color microarray data including signal intensity, background correction, uniformity of the expression ratio over the chip surface (within-array normalization), and normality of M-value distributions were evaluated according to Smyth and Speed (2003). M-value was defined as the logarithm in base-2 of water-deficit versus control expression ratio. Reproducibility between replicates that were assessed indicated that the experimental system provided consistent signals in spots corresponding to the same gene and acceptable low variability between biological replicates (not shown). P-values associated to the statistical analysis of differential expression obtained from Limma analysis are corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) procedure (Benjamini & Hochberg, 1995). Differences in gene expression were considered to be significant when the M-value was higher than 0.7 (absolute value) and the FDR-adjusted P-value was smaller than 0.05.
2012-10-05 | E-GEOD-41309 | biostudies-arrayexpress
Project description:Whole-genome duplication, or polyploidy, is common in many plant species and often leads to better adaptation to adverse environmental condition. However, little is known about the physiological and molecular determinants underlying adaptation. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological experiments to study root-shoot communication associated with gene expression studies in roots and leaves were performed. V/4xRL was much more tolerant to water deficit than V/2xRL. Gene expression analysis in leaves and roots showed that more genes related to the response to water stress were differentially expressed in V/2xRL than in V/4xRL. Prior to the stress, when comparing V/4xRL to V/2xRL, V/4xRL leaves had lower stomatal conductance and greater abscisic acid (ABA) content. In roots, ABA content was higher in V/4xRL and was associated to a greater expression of drought responsive genes, including CsNCED1, a pivotal regulatory gene of ABA biosynthesis. We conclude that tetraploidy modifies the expression of genes in citrus roots to regulate long-distance ABA signaling and adaptation to stress. Transcriptional profiling of sweet orange (Citrus sinensis) scion leaves comparing control untreated with water deficit conditions. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological studies showed that V/4xRL was much more tolerant to water deficit than V/2xRL. Global gene expression changes induced by water deficit were monitored in the leaves of V/2xRL and V/4xRL by microarray hybridization. The Citrus genome-wide cDNA microarray was used, which includes 21,081 putative unigenes described in Martinez-Godoy et al. (2008). Two independent microarray hybridization experiments with leaves of the 2x Valencia Delta orange alternatively grafted onto 2x or 4x RL rootstocks were respectively performed. For each experiment, the Cy-labelled cDNA of control leaves was hybridized with labelled cDNA from water-stressed samples. To avoid Cy3 and CY5 dye-related artefacts, control and water-stressed cDNA samples were dye-swapped and used to hybridize four slides corresponding to different combinations of the four biological replicates obtained from every treatment. The microarray hybridizations were performed according to Allario et al. (2011). A GenePix 4000B microarray scanner (Axon Instruments, Inc.) and the GenePix Pro 4.1 acquisition software were used to scan the chips at 5-10 M-BM-5m resolution. Photomultiplier gains for the two channels were adjusted so that the ratio of total intensities was approximately 1 and the percentage of saturated spots was about 1%. High-resolution tiff images were generated and used for quantification of gene expression data. Spot positions were identified on the colour images and quality flags were assigned to individual spots both automatic and manually. Only spots with background-subtracted foreground intensity greater than two in at least one channel were used, and only microarrays with optimal hybridization data were pre-processed and normalized for further analyses. Raw data were imported into the R computing environment for pre-processing, visualization, and statistical analysis. To identify probes showing significant differential gene expression between samples, the Linear Models in Microarrays (LIMMA; Smyth, 2005) software package was used. Pre-processing and normalization of two-color microarray data including signal intensity, background correction, uniformity of the expression ratio over the chip surface (within-array normalization), and normality of M-value distributions were evaluated according to Smyth and Speed (2003). M-value was defined as the logarithm in base-2 of water-deficit versus control expression ratio. Reproducibility between replicates that were assessed indicated that the experimental system provided consistent signals in spots corresponding to the same gene and acceptable low variability between biological replicates (not shown). P-values associated to the statistical analysis of differential expression obtained from Limma analysis are corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) procedure (Benjamini & Hochberg, 1995). Differences in gene expression were considered to be significant when the M-value was higher than 0.7 (absolute value) andthe FDR-adjusted P-value was smaller than 0.05.
2012-10-05 | E-GEOD-41310 | biostudies-arrayexpress
Project description:Citrus, one of the world’s most important crops is facing considerable challenges due to drought events. Previous studies have demonstrated that tetraploid rootstocks exhibit greater tolerance to abiotic stresses than their diploid counterparts. The effects of combining tetraploid rootstock with a triploid scion under water deficit treatment have not been thoroughly explored. A water deficit experiment was conducted in pot using four citrus scion/rootstock combinations: diploid and tetraploid Swingle citrumelo rootstocks grafted with diploid Mexican Lime and triploid Persian lime. Physiological, biochemical, and transcriptomic analyses revealed that scions grafted onto tetraploid rootstocks had significantly better drought tolerance, especially when combined with triploid Persian lime. This improved resilience was linked to enhanced water regulation, higher photosynthesis, increased stomatal conductance and transpiration during water stress. Elevated abscisic acid levels and stronger antioxidant activity in polyploid rootstocks further contributed to stress response. Transcriptomic data showed notable gene expression changes, providing insights into drought tolerance mechanisms. These findings underscore ploidy’s role at both the rootstock and scion levels in shaping the plant’s response to water deficit, revealing useful interactions between rootstock and scion influencing drought resilience. This study highlights the potential for leveraging polyploid rootstocks and scions to improve drought tolerance in citrus cultivation.
2025-05-12 | GSE255759 | GEO
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.
2017-12-31 | GSE89185 | GEO
Project description:In horticulture, grafting is a popular technique used to combine positive features of two different plants, obtained by joining a scion (generally the part above the ground) onto a rootstock (constituted by the stem and roots). Despite its wide-use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype are not fully understood. Given that epigenetics is an important component of distance signalling in plants, we investigated the genome wide changes in the DNA methylation induced in eggplants grafted onto two interspecific rootstocks commercially used to induce scion vigour, compared to self-grafted plants. We found that vigour was associated to a specific change in scion gene expression and a genome wide hypo-methylation in CHH context. Interestingly, this hypomethylation correlated with downregulation of younger and potentially more active LTR retrotransposons. Our data indicate that graft-induced epigenetics modifications are associated to both physiological and molecular phenotypes in plants, and suggest that rootstocks can induce vigour by reducing DNA methylation in the scion genome, similarly to what observed in some heterotic hybrids.
2021-09-30 | GSE136784 | GEO
Project description:In horticulture, grafting is a popular technique used to combine positive features of two different plants, obtained by joining a scion (generally the part above the ground) onto a rootstock (constituted by the stem and roots). Despite its wide-use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype are not fully understood. Given that epigenetics is an important component of distance signalling in plants, we investigated the genome wide changes in the DNA methylation induced in eggplants grafted onto two interspecific rootstocks commercially used to induce scion vigour, compared to self-grafted plants. We found that vigour was associated to a specific change in scion gene expression and a genome wide hypo-methylation in CHH context. Interestingly, this hypomethylation correlated with downregulation of younger and potentially more active LTR retrotransposons. Our data indicate that graft-induced epigenetics modifications are associated to both physiological and molecular phenotypes in plants, and suggest that rootstocks can induce vigour by reducing DNA methylation in the scion genome, similarly to what observed in some heterotic hybrids.
2021-09-30 | GSE136783 | 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.
2024-07-10 | GSE263656 | GEO
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.
2015-03-19 | GSE66391 | GEO
Project description:The purpose of this project is to examine the effects of rootstocks on the gene expression patterns in scions of apple trees. Gene expression patterns were examined in the Gala variety grafted onto seven different, commonly used rootstocks. These trees were grown in the greenhouse to limit environmental effects. Also, gene expression profiles were examined in three different varieties (Ambrosia, Melrose,and Gala) grafted onto B.9 rootstocks grown in the field. Keywords: apple, rootstock, graft, scion
2006-05-05 | GSE4762 | GEO
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. Previously, we reported a combination of Penicillin G and Streptomycin was effective in eliminating or suppressing the associated bacterium, M-bM-^@M-^XCandidatus Liberibacter asiaticusM-bM-^@M-^Y (Las). Here we report the bacterial composition and community structure in HLB-affected citrus plants during a growing season and while being treated with antibiotic combinations PS (Penicillin G and Streptomycin) and KO (Kasugamycin and Oxytetracycline) using the PhylochipM-bM-^DM-" G3 array. The antibiotic treatments were conducted on the randomized complete block design with four replicates. For each replicate, five HLB-affected, 7-year-old citrus trees (a unique hybrid, 10c-5-58, which is an open-pollinated seedling from the combination of Lee mandarin M-CM-^W Orlando tangelo) at the USHRL farm, 10 cm in diameter, were injected with either 100 ml of the antibiotic combination treatment PS (5 g of penicillin G potassium + 0.5 g of Streptomycin per tree) or the antibiotic treatment KO (2 g of oxytetracycline + 1.0 g of kasugamycin per tree). Five trees were injected with water as injection controls (CK). Injections were made using an Avo-Ject syringe injector (a catheter-tipped 60 ml syringe; Aongatete Coolstores Ltd., NZ) beginning in August of 2010. The tapered tip was firmly fitted into a 19/64-in (7.5 mm) diameter hole, M-bM-^IM-^H3 cm deep, drilled into the tree. The injector was kept in the tree and the treatment lasted for one week in each injection-trunk. Treatments were repeated every 2 months for one year and ceased in August of 2011. Before and during treatment more than 30 leaf samples per tree were taken from different positions around the tree canopies for qPCR assays at 2 month intervals.DNA for the PhyloChipM-bM-^DM-" G3 analysis, which was extracted from 20 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-46727 | biostudies-arrayexpress