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

Cold stress is one of the environmental factors limiting productivity and geographical distribution of crops. To determine functional annotation and differential gene expressions of plants under cold stress, 3127, 1188, and 2292 expressed sequence tags (ESTs) respectively from low temperature- treated seedlings of rice, wheat, and barley was 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 that had important hits in the protein database of Arabidopsis. All of the unigenes with significant hits were grouped with MapMan software. In three functional groups including 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 between the three plants under cold stress by assembling all of the ESTs, which resulted 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 coding region of the candidate genes, showed a variety of 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.