Comparative transcriptome analysis between two tomato materials under salt stress
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE148353 | GEO | 2020/04/10
REPOSITORIES: GEO
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Project description:RNA sequencing was performed to investigate the the response mechanism of tomato response to drought stress. C2H2-type zinc finger proteins are classic and extensively studied members of the zinc finger family. C2H2-type zinc finger proteins participate in plant growth, development and stress responses. In this study, 99 C2H2-type zinc finger protein genes were identified and classified into four groups, and many functionally related cis-elements were identified. Differential C2H2-ZFP gene expression and specific responses were analyzed under drought, cold, salt and pathogen stresses based on RNA-Seq data. Thirty-two C2H2 genes were identified in response to multiple stresses. Seven, 3, 5, and 8 genes were specifically expressed under drought, cold, salt and pathogenic stresses, respectively. Five glycometabolism and sphingolipid-related, pathways and the endocytosis pathway were enriched by KEGG analysis. The results of this study represent a foundation for further study of the function of C2H2-type zinc finger proteins and will provide us with genetic resources for stress tolerance breeding.
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Project description:Comparative transcriptome analysis between two tomato materials under salt stress
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Project description:Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium ‘PI365967’ is significantly more salt-tolerant than a cultivar, Solanum lycopersicom ‘moneymaker’. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2.
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Project description:Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium M-bM-^@M-^XPI365967M-bM-^@M-^Y is significantly more salt-tolerant than a cultivar, Solanum lycopersicom M-bM-^@M-^XmoneymakerM-bM-^@M-^Y. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2. In one treatment, 9 six-leaf-old plants of one tomato genotype (PI365967 or Moneymaker) were divided into three biological replicates and treated hydroponically under sterile condition with (or without) 200 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip, resulting in 12 chips in total.
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Project description:Comparative transcriptome analysis between two tomato materials under drought stress
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Project description:High salinity is one of the most serious threats to crop production. To 1 better understand the molecular basis of plant responses to salt stress, we combined suppression subtractive hybridization (SSH) and microarray approaches to identify the potential important or novel genes involved in salt tolerance. First, SSH libraries were constructed for two cultivated tomato (Solanum lycopersicum) genotypes: LA2711, a salt tolerant cultivar, and ZS-5, a salt sensitive cultivar, to compare salt treatment and non-treatment plants. Then a subset of clones from these SSH libraries were used to construct a tomato cDNA array and microarray analysis was carried out to verify the expression changes of this set of clones upon salt treatment at various time points compared to the corresponding non-treatment controls. A totalof 201 non-redundant genes differentially expressed upon 30 min of salt stress treatment either in LA2711 or ZS-5 were identified from microarray analysis, most of which were not previously associated with salt stress. The diversity of the putative functions of these genes indicated that salt stress resulted in a complex response in tomato plants. Keywords: gene expression, genotype, microarray, salt stress, SSH, tomato
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Project description:Large-scale gene expression affected by salt stress was analyzed with tomato seedlings (Lycoperson esculentum Mill cv. Money Maker) by a cDNA microarray (Tom1). The significantly differentially expressed genes (5% Benjamini-Hochberg false discovery rate) consisted of 1757 sequences in the analyzed tissues (cotyledons + shoot tip). Genes with over 2 fold difference were selected from the list and further categorized into different function and cellular processes. Tomato homologous genes for the chaperone proteins, antioxidant enzymes (catalase and peroxidase), and ion transporters (Na+-driven multidrug efflux pump, vacuolar ATPase, and others) were induced. The ACC oxidase and ethylene-responsive gene tomato homologs had higher transcript level after salt treatment. Multiple members with different expression patterns were identified for the bZIP, WRKY, and MADS-box transcription regulator. Different genes in the signal transduction pathway, such as the protein kinases (Shaggy kinase, mitogen-activated protein kinase, ethylene receptor neverripe, and others), protein phosphatases, calmodulin, G-protein, and the N- myristoyltransferase, were regulated by salt stress. Most of the protease and the inhibitor homologs were suppressed by salt stress. In addition, different isoforms of cytochrome P450, genes for polyamine biosynthesis (putrescine and proline) and detoxification compounds (glutathione and thioredoxin), several key enzyme genes in the metabolic pathways of carbohydrates, amino acids, and fatty acids, were also affected by salt treatment. This study has provided a set of candidate genes, especially those in the regulatory machinery that can be further investigated to define salt stress in tomato and other plant species. Keywords: treatment response
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