Far-red enriched light delays tomato transcriptome modulations in response to Botrytis cinerea infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE157831 | GEO | 2020/09/30
REPOSITORIES: GEO
Similar Datasets
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1) Keywords: strain_or_line_design
2007-01-22 | GSE6169 | GEO
Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana. Plants were exposed for 2 h. to the following treatments: high R/FR with mock spray, low R/FR with mock spray, high R/FR with JA spray, low R/FR with JA spray. Gene expression was determined in petioles.
2012-04-30 | E-GEOD-35700 | biostudies-arrayexpress
Project description:Plants were germinated in white light and then either grown in WL (white light) or far-red enriched white light (WL+FR)
2020-02-03 | GSE137009 | GEO
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1)
2022-11-21 | E-NASC-41 | biostudies-arrayexpress
Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana.
2012-05-01 | GSE35700 | GEO
Project description:This study provides a comparison of gene expression in two tomato cultivars, Moneymaker and M82, focusing on first internode and its innermost cell type pith—under two light conditions: white light with far-red supplementation (WL+FR) and the control condition of white light (WL). The samples were harvested at four time points leading to the point where internode elongation could be measured in response to WL+FR. The timepoints were 6, 24, 30, and 48 hours after treatment initiation.
2024-02-29 | GSE255611 | GEO
Project description:Jasmonate (JA) signaling plays a key role in mediating both resistance and susceptibility to the root-infecting fungal pathogen Fusarium oxysporum. Within this system, the roles of the JA-signaling repressor gene family of JASMONATE ZIM-domain (JAZ) genes had not been investigated. By screening JAZ T DNA insertion lines for altered resistance or susceptibility to F. oxysporum, we identified a JAZ7 mutant (jaz7-1D) highly susceptible to F. oxysporum infection. Further analyses revealed jaz7-1D exhibits constitutively active JAZ7 expression, enhanced expression of JA-defense marker genes, and increased sensitivity to JA-inhibition of root elongation. To further explore altered JA-signaling and JA-responses in this mutant, we use whole transcriptome profiling of jaz7-1D versus wild-type (Col-0) plants after mock/control and JA treatment.
2016-02-08 | GSE61884 | GEO
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1) Experiment Overall Design: Number of plants pooled:300 seedlings
2008-06-14 | E-GEOD-6169 | biostudies-arrayexpress
Project description:This project aimed to understand the interplay between light signalling, transzeatin signalling and nitrogen availability on hypocotyl elongation responses. To do so, mRNAseq on shoots was performed, with the following variables studied in all possible combinations: Genotypes: Wild-Type (Col-0), abcg14 (Ko et al., 2014), cypDM (cyp735a1,a2, Kiba et al., 2013) Light quality: White Light (WL, R:FR=2.5), White Light + Far Red light (WL+FR, R:FR=0.25) Nitrate availability: High Nitrate (HN, 10mM KNO3), Low Nitrate (LN, 0.2mM KNO3) Plants were grown for 4 days under WL conditions (16 h light : 8 h dark, PAR=150, 70% humidity, R:FR=2.5 at 20°C) and on the different nitrate conditions. Plants from the WL+FR (R:FR=0.25) samples were treated at ZT 8 for 90min with WL+FR prior the collection of shoots.
2024-09-19 | E-MTAB-13638 | biostudies-arrayexpress
Project description:This experiment was designed to uncover the transcriptomic changes that would occur in rice after 24 h of supplemental FR treatment, in an accession dependant manner. To do so, 6 different varieties of rice (IR64, Nipponbare, Luk Takhar, M Blatec, Mudgo, Sabharaj and Zhenshan) were grown in the greenhouse facilities of the Botanical Gardens, Utrecht University, in The Netherlands, in summer and autumn of 2021. After five days in WL (400 µmol m-2 s-1 of combined sunlight and artificial light), the treatment group was exposed to supplemental FR (500 µmol m-2 s-1 FR, R:FR of 0.2) light for 24 hours. The whole shoot was sampled, with four plants pooled in one sample. The experiment was repeated four times, resulting in 48 samples (6 varieties x 2 treatments x 4 replicates). Same samples were run on two individual lanes.
2024-04-24 | E-MTAB-13023 | biostudies-arrayexpress