S. Hochreiter and R. Wagner (Eds.): BIRD 2007, LNBI 4414, pp. 48–65, 2007. © Springer-Verlag Berlin Heidelberg 2007 Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets Angelica Lindlöf 1 , Marcus Bräutigam 2 , Aakash Chawade 2 , Björn Olsson 1 , and Olof Olsson 2 1 School of Humanities and Informatics, University College of Skövde, Box 408, 541 28 Skövde, Sweden 2 Dept. of Cell and Molecular Biology, Göteborg University, Göteborg, Box 462, 403 20 Göteborg, Sweden {angelica.lindlof, bjorn.olsson}@his.se, {marcus.brautigam, aakash.chawade, olof.olsson}@molbio.gu.se Abstract. Freezing tolerance in plants is obtained during a period of low non- freezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and time- efficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses. 1 Introduction Cold acclimation is a biological process that increases freezing tolerance of an organism, which prior to exposure to sub-zero temperatures is subjected to cold stress at temperatures between 0-10ºC [1-6]. Many species have this ability to acclimate to cold and thereby survive harsh winter conditions. In nature, the tolerance is obtained