Transcriptional regulation research in tomato roots
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Solanum lycopersicum
SUBMITTER: Junyu Bai
PROVIDER: E-MTAB-14084 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2023-03-11 | PXD039195 | Pride
Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.
2014-03-01 | E-GEOD-53995 | biostudies-arrayexpress
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Project description:The Arabidopsis thaliana NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), acts as a master regulator for differentiation of xylem vessels. In order to identify a set of genes regulated by VND7, we carried out a microarray experiment with the Arabidopsis full-genome GeneChip array ATH1 (Affymetrix) for transgenic Arabidopsis roots overexpressing VND7. Experiment Overall Design: Total RNAs were isolated from roots of 5-day-old seedling of transgenic plants overexpressing YFP and VND7-YFP under control of Cauliflower mosaic virus 35S promoter. Three independent biological replicates were performed for each sample.
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Project description:Changes in gene expression during adaptation to abiotic stress conditions in the barley roots.
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Project description:Tomato, a Strategy I model plant for Fe deficiency, is an important economical crop. The transcriptional responses induced by Fe deficiency in tomato roots were previously described (Zamboni et al., 2012). The changes in trascriptome caused by the supply of Fe to plants starved fro 1 week were described in relation to the different nature of chelating agents (Fe-WEHS, Fe-CITRATE and Fe-PS). Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron (0 μM Fe-EDTA) for 1 week and supplied for 1 h with 1 μM of Fe as Fe-WEHS (supply_Fe_WEHS), Fe citrate (supply_Fe_CITRATE) and Fe-PS (supply_Fe_PS). Tomato plants were hydroponically grown in all three case of Fe supply. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).
2016-01-11 | E-GEOD-69419 | biostudies-arrayexpress
Project description:Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to deciphered the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found that there is an over-abundant proteins relevant to Nitrate and amino acids metabolisms in the Salt-tolerant cultivars. The significant increase in expression of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. And the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including Sterol side chain reductase, gamma aminobutyrate transaminase and Starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future
2022-02-08 | PXD029130 | Pride
Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3â?¢6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq. Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance. Examination of mRNA levels in control and Al-treatment roots of C. grandis and C. sinensis with two biological replicates were generated by deep sequencing, using Illumina HiSeq 2000 device.
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