African Journal of Environmental Economics and Management ISSN: 2375-0707 Vol. 5 (4), pp. 316-327, May, 2017. © International Scholars Journals

Full Length Research Paper 

Microarray analysis of genes affected by salt stress in tomato

Suping Zhou1, Shu Wei2, Braden Boone3 and Shawn Levy1

1Institute of Agricultural and Environmental Research, Tennessee State University, 3500 John A Merritt Blvd, Nashville,

TN37209, USA.

2Plant Biology Department, University of Minnesota, St Paul, MN 55108. USA.

3Vanderbilt Microarray Shared Resource, Vanderbilt University,465 21st Avenue South, MRBIII Room 9274, Nashville, TN 37232, USA.

*Corresponding author. E-mail: zsuping@tnstate.edu

Accepted 15 August, 2007

Abstract

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.

Key words: Antioxidants, cellular metabolism, cell wall, chaperonine, ethylene, protein kinase, tomato, transcription regulator, translation regulator, salt stress.