In silico prediction of cold responsive genes in canola by comparative genomics using Arabidopsis thaliana

Low temperature is an important abiotic stress limiting the production and geographical dispersion of many crops, including rapeseed, as an important oil crop. In this study, known cis-elements regulating molecular responses of plant to cold stress were used to identify genes involved in cold tolerance. From 62,384 Unigenes from Brassica Genome Gateway, 56 cold responsive genes were identified. Promoter analysis, gene ontology enrichment, co-occurrence, protein- protein interaction and in silico gene expression analysis were performed to validate the results of gene identification. The results showed known cis-element appearance in promoter region of all identified genes which involved in different biological pathways such as Calvin cycle, respiration and signal transduction in different cell parts. Co-occurrence study of identified genes illustrated mutual connections of genes with correlations above 0.64. Promoter analysis, PPI network and investigating transcription factors involved in transcription regulation of 56 identified genes and 98 co-expressed genes indicated the molecular mechanisms and similar pathways of plant response to cold and introduce candidate genes to be used in breeding and genetic engineering programs.