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Identification of salt stress regulated genes in tomato seedlings by SSH and microarray analysis

ABSTRACT: 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

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE4961 | GEO | 2007/01/09

SECONDARY ACCESSION(S): PRJNA96715

REPOSITORIES: GEO

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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 Effect of 75mM NaCl on gene’s expression in tomato seedlings, Lycoperscon esculentum Mill. cv. Money Maker after 17 d of treatment. Each sample represents a pool of same tissue 20 seedlings grown in two flasks. Experiment was done in triplicate.

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Identification of salt stress regulated genes in tomato seedlings by SSH and microarray analysis

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