Cross hybridization to Arabidopsis thaliana array reveals cold stress responsive genes in Lepidium latifolium

Cross species hybridization is an attractive option to understand the regulatory mechanisms and transcriptional networks underlying a biological activity, particularly for a non model organism. We have used the same approach to idenitfy cold responsive differentially expressed genes (DEGs) in Lepidium latifolium using Arabidopsis thaliana cDNA array chip. In all, 1315 DEGs were discovered. Putative functions of these cold-responsive genes were explored based on annotations using TAIR database and Blast2GO. Most of the up-regulated gene products were mapped to nucleus (20%) and plastids (15%) showing higher activities as DNA binding proteins, i.e., transcription factors. In all, 45 genes encoding transcription factors were identified belonging most frequently to AP2 family proteins (Seven genes) followed by NAM domain containing proteins (Five genes). Transcription factor binding sites (TFBS) were predicted for 1,100 genes belonging to 78 clusters of co-expressed genes. Interestingly, 50% of these regulatory sites contained a microsatellite repeat. Considering, Lepidium to be a native of high altitude cold regions, the genes identified in this study can be of wide importance to agricultural biotechnologists.