Comparative Analysis of Expressed sequence tags in Wheat, Rice, and Barley under Cold Stress

Document Type : Research Paper


1 a)Department of Plant Production and Genetics, Faculty of Agriculture, Zanjan University, Zanjan, Iran. b) Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

2 Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran

3 a) Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. b) Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Germany


Cold stress is an environmental factor limiting crop productivity and geographical distribution. To determine functional annotation and differential gene expressions of plants under cold stress, 3127, 1188, and 2292 expressed sequence tags (ESTs) from low temperature-treated rice, wheat, and barley seedlings, respectively, were analyzed. The ESTs from each library yielded 1995 (rice), 950 (wheat), and 1831 (barley) unigenes. BLASTX revealed 1458 (rice), 703 (wheat), and 1324 (barley) unigenes with important hits in the protein database of Arabidopsis. All the unigenes with significant hits were grouped with MapMan software. In the resulting three functional groups, photosynthesis, nucleotide metabolism, and signaling categories, a significant difference was observed between the transcripts of rice and barley under cold stress. We identified differentially expressed genes from the three plants under cold stress by assembling the ESTs, resulting in 1101 contigs. There were 12 genes identified that had significantly different expressions between the three libraries. Promoter analysis of a 1500-bp sequence upstream of the candidate genes' coding region showed various regulatory elements with different roles. The existence of elements involved in various stresses in the promoter regions of candidate genes confirmed the role of these genes in stress responses. The identified genes could be putative candidates for gene manipulation to improve the cold tolerance of valuable crop plants.


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